Bioscience Reports, Vol. 9, No. 2, 1989
H Y P O THESIS
A Unified Matrix Hypothesis of DNADirected Morphogenesis, Protodynamism
and Growth Control 1'2
Klaus Scherrer
Received October, 1988
A theoretical concept is proposed, in order to explain some enigmatic aspects of cellular and
molecular biology of eukaryotic organisms. Among these are the C-value paradox of DNA
redundancy, the correlation of DNA content and cell size, the disruption of genes at DNA level, the
"Chromosome field" data of Lima de Faria (Hereditas 93:1, 1980), the "quantal mitosis" proposition
of Holtzer et aL (Curr. Top. Dev. Biol. 7:229 1972), the inheritance of morphological patterns, the
relations of DNA and chromosome organisation to cellular structure and function, the molecular basis
of speciation, etc. The basic proposition of the "Unified Matrix Hypothesis" is that the nuclear DNA
has a direct morphogenic function, in addition to its coding function in protein synthesis. This
additional genetic information is thought to be largely contained in the non-protein coding transcribed
DNA, and in the untranscribed part of the genome.
KEY WORDS: matrix hypothesis; morphogenesis; protodynamics; growth control; DNA; genome
organisation; gene expression; gene regulation.
"In this world, seeds of different kinds, sown at the proper time in the land, even in one field, come
forth (each) according to its kind."
Manusmriti (9 : 38)
INTRODUCTION
This theoretical essay represents an attempt to correlate rationally some
enigmatic aspects of two domains of Cell Biology which, in general, are treated
separately. These are cellular morphology and organisation on the one hand, and
Institut Jacques Monod, Universit6 PARIS VII, 2 Place Jussieu, F 75251 Paris Cedex 05, France.
1 In the biological sense, the term "Matrix" is used here to signify the integrity of the cell's fibrous
networks in nucleus and cytoplasm, during interphase and metaphase. In the philosophical sense,
"Matrix Hypothesis" integrates also the etymological meaning of the term, which stems from
"mater" (i.e. origin), and means also a lattice within a frame of coordinates, or else: "Something (as
a surrounding or pervading substance or element) within which something else originates or takes
form or develops" (cf. Webster's Intern. Dict.).--The term "Protodynamism" was defined earlier
(Scherrer, 1966) as meaning the integrity of the organised movements of the cellular components,
excluding mere diffusion.
2 A preliminary version of this assay was published previously (cf. Scherrer, 1985).
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0144-8463/89/0400-0157506.00/0~ 1989 Plenum Publishing Corporation
158
Scherrer
the organisation and function of genomic D N A on the other. The hope is to show
some perspectives of understanding which may serve as a basis for future
experimental and theoretical investigation. As such, this essay will necessarily
appear superficial to specialists in both domains under consideration. However,
as demonstrated 20 years ago by the "Cascade Regulation Hypothesis" (Scherrer
and Marcaud, 1968; Scherrer, 1980), in an early attempt to draw attention to
importance and complexity of post-transcriptional controls in eukaryotic cells, it
is sometimes necessary to penetrate beyond the incomprehendable mass of details
to the underlying general patterns, in spite of the initial oversimplification.
The present reflection originated from the experimental observation of the
systematic punctuation of the eukaryotic D N A by AT-rich D N A segments
(Moreau et al., 1981) having precise locations in relation to genes (Moreau et al.,
1982) and acting essentially as spacers (review in Scherrer and Moreau, 1985).
This led us to explore possible theoretical explanations of this surprising
phenomenon of long range D N A organisation. These independently evolving
ideas were found to converge partially with others, for example those exposed in
a theoretical analysis by Cavalier-Smith (1978) about the C-value paradox
(Thomas, 1971). The present discussion develops some ideas which possibly
extend that anterior work, but is developed from a more mechanistic viewpoint of
Molecular Biology, and attempts to integrate as much as possible related
knowledge, thus far dispersed in between several domains of investigation.
The central propositions of the present "Unified Matrix Hypothesis" are based
on the idea that there exists, in addition to the genetic code of protein synthesis, a
system of genetic information encoded into the cellular D N A which has a direct
morphogenic and organisational function. Based on a system of signals, obeying a
novel code of recognition and involving protein-nucleic acid interactions, its
essential information content relies on the meaning of these signals and their
topology of distribution within the DNA; in such a system, mere amounts of D N A and
relative DNA length represent genetic information.
Morphogenesis of organism and organ is necessarily based on properties of
the individual cell, essentially the number and direction in space of consecutive
cell divisions in a clone, modulated by cell to cell interaction. In some cases at
least it is evident that this process must be based on the morphology of the
individual cell and on its functional organisation (e.g. the salivary gland of
Drosophila). How these properties arise is, however, a complete mystery at
present. Some think that genes are not of primary importance in morphogenesis
(Lima de Faria, 1983); morphogenesis seems to be based to a large extent on the
self-assembly of DNA-encoded proteins and their enzymatic derivatives. Examples are some of the matrix networks, in particular the tubulin fibers which
self-assemble even in vitro. Although variable co-polymerisation of several
different components may allow for some modulation in the assembly of such
structures, the generation of the complexity and specificity of the individual
phenotype of cell and organ seems, however, to be beyond the limits of the
possible application of this kind of process. That matrix fibers are involved in
cellular and extracellular architecture is unquestionable (cf. Berezney, 1984; also
a recent review volume of J. Cell. Biol. and in particular Fey et al. (1984)
Unified Matrix Hypothesis
159
therein); however what directs their assembly, their overall organisation and
specificity? The enigma seems still complete.
A quite different enigma relates to the genomic D N A in eukaryotes. To put
it simply: there is too much of it and of the wrong kind! Calculations show that no
more than a few percent of typical eukaryotic D N A can be accounted for by
structural genes. To make matters worse, animals and plants of comparable
morphology may contain vastly different amounts of D N A (the so-called C-value
paradox, Thomas, 1971) or, apparently, different kinds of DNA. Recent studies
show that plant cells may contain anywhere from 0.6 pg to 35 pg of haploid D N A
(Ranjekar et al., 1978; and personal communication, 1983) per nucleus, and
amphibians 3 pg-100 pg (Rosbash et al., 1974; Sommerville, 1977). Crabs have up
to 90%, mice about 6% of AT-rich satellite DNA, whereas rats are apparently
devoid of this kind of DNA. The comparison of the D N A of Triturus and
Xenopus shows that the about seven fold difference in D N A content does not
concern unique frequency D N A transcribed into pre-mRNA and mRNA but
repetitive D N A of all frequency classes (Rosbash et al., 1974). In plants the
difference concerns neither simple sequence (highly repetitive), nor unique
(coding?) DNA, but the intermediate frequency class and, in particular, its
AT-rich fraction (Ranjekar, personal communication, 1983; cf. Bhave et al.,
1984).
We have found that eukaryotic D N A is systematically punctuated by AT-rich
DNA segments (Moreau et al., 1981) which frame units of genome organisation
(Moreau et al., 1982), of transcription (Broders and Scherrer, 1987) and
eventually genes and gene fragments (exons) in pre-mRNA. Integrating the
known facts about these AT-rich elements in eukaryotic D N A discussed
elsewhere (Scherrer and Moreau, 1985), we are again faced by the old dilemma
concerning eukaryotic DNA, that of "too much" (uneconomical!) and "of the
wrong kind" (no reading frames), a dilemma exposed most concisely by the
C-value paradox mentioned above (cf. e.g. review in Cavalier-Smith, 1978). So
why does nature insist on piling up "unnecessary" D N A when scientists feel that
the cell does not need it? It must be "junk" D N A (Ohno, 1972) or worse, a kind
of perversion of the "selfish" D N A (Doolittle, 1982)! The attempt ro overcome
this intellectual deadlock must obviously consider the proposition that other
possible functions may be ascribed to the surplus DNA; this is one of the main
objectives of the Matrix Hypothesis developed here.
If we begin by rejecting the a priori notion that all of this "junk" D N A is
useless, and take more seriously what would otherwise be considered as spurious
coincidence (and this choice is possibly rather a "philosophical" question or
attitude) then a dual pattern of possible significance of this D N A seems to
emerge. It relates to the architecture of cell and chromosomes and their
"mechanics" on the one hand, and to cellular topology and "protodynamism" in
the widest sense on the other. In other words: within the Unified Matrix
Hypothesis the "extra" D N A is postulated to relate to the structural and dynamic
organisation of the cell, and to morphogenesis.
The incredible speed and flexibility of movement of the cellular components
often opposes the concepts of a static internal architecture. Biochemists and
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Scherrer
Molecular Biologists have a tendency to view the cell as a "glorified test-tube".
Furthermore, the concept of high mobility of cellular macromolecular components has spread over to the genome itself. We are witness to a literal
"dissolution" of the rigid genome organisation, brought about by natural or
experimental gene mobility, DNA transposition and translocation. However,
although genes seem to be able to move most rapidly from place to place, and
although it is possible to achieve experimentally the expression of almost any
gene in any host, the fact is that within a species the genome organisation is
remarkably conserved.
In living matter the seemingly static architecture is thus just a temporary
facet of its dynamic organisation. And the variability and mobility of genes and
DNA sequences at the level of the genome may be considered as a prerequisite
for the generation of the more stable variants of organisation specific to a species,
and to its somatic "genotype" (i.e. DNA organisation) and eventually phenotype.
And the question arises as to what extent these two aspects of the cell's
physiology might relate and condition each other.
The central proposition of the Matrix Hypothesis to be developed here is the
consideration that the non-protein coding part of the cell's genomic DNA might
govern largely and directly the cell's architecture and dynamic organisation. The
concept that the role of DNA is to produce enzymes and proteins and their
derivatives, which might eventually self-assemble in a para-cristalline manner, is
extended to include the idea that the non-protein-coding part of the DNA may
directly dictate the assembly of cellular components into a matrix network which
then becomes the core of the cell's static and dynamic architecture. This idea
differs from the proposition of Cavalier-Smith (1978) to the extent that the DNA
is not considered to be itself a nuclear skeleton but acts as a template to build the
matrix network, constituted of protein and possibly RNA, which eventually
becomes independent of the DNA. This proposition does not exclude but rather
complements the mechanism of protein self-assembly, which is all-evident in
some precise cases. Finally, some deductions of the Matrix Hypothesis seem to
have the potentiality to account logically for the excessive amounts and variations
in DNA content in different species and its possible rearrangment in
differentiation, and to project some intrinsic logic into some seemingly absurd
features of eukaryotic DNA, such as the fragmentation of the gene and the
necessity for its post-transcriptional reconstitution.
In the following we will formulate several propositions included in this
scheme and discuss later their experimental and theoretical background.
THE BASIC POSTULATES
OF T H E U N I F I E D M A T R I X H Y P O T H E S I S
(1) The extra-genic, non-protein-coding part of genomic DNA governs organisation and assembly of the cellular matrix; the topology of specific sites
in the DNA involved in matrix-protein : DNA interaction determines directly
the extent and topological organisation of the matrix network into which, in
turn, the DNA is suspended. The topology of these sites and hence mere
UnifiedMatrix Hypothesis
(2)
(3)
(4)
(5)
(6)
(7)
(8)
(9)
161
DNA length in between individual sites amounts to a novel type of genetic
information.
To allow for a predefined three-dimensional structure in which specific
proximal or distal segments in the DNA are joined at specific points of the
matrix, the DNA:matrix-protein interaction is governed by a specific code
involving combinations of pleiotropic signals; as a consequence, such DNA
sequences tend to be repetitive, and matrix proteins will be only partially
specific to a gene domain, to a cellular sector or a tissue.
The DNA not only determines cellular and nuclear volume (cf. CavalierSmith, 1978) but also cell morphology, and organizes the skeletal structures
in early stages of lineage determination, when the nuclei of stem cells
virtually fill the cellular lumen.
In crucial steps of differentiation, the decondensed DNA of specific gene
domains, genes or gene fragments, condition the build-up of local matrix
networks, which when integrated, define overall somatic cell morphology
and volume. Genes are thus placed in specific topological sectors of the
matrix, of the cell and nucleus; the necessity to keep this topology
genetically stable leads to a relatively stable localisation of genes in the
chromosomal DNA, conditioning the "Chromosome Field" (Lima de Faria,
1980).
Extra-genic and intra-genic transcribed DNA spacers interact in a genespecific manner With specific matrix "channels" and condition and support
cell-sector specific processing and transport of pre-mRNA; in turn the
pre-mRNA contains signals conditioning build-up and dynamism of gene
specific matrix channels on which its processing occurs (Maundrell et al.,
1981). The organisational principle of a specific cell's dynamic architecture
and RNA processing and transport system ("Protodynamism") is hence
thought to be conditioned directly by DNA and pre-mRNA itself.
Chromosomes are held in specific positions relative to each other during
inter- and metaphase by direct DNA and protein mediated interaction,
ectopic pairing and matrix elements.
A pattern of point to point alignment of the sister chromatids during meiotic
and mitotic recombination and sister chromatid exchange, allows for
crossing-over at specific topologically fixed sites of the DNA; this
topology--relating to the cells genome and morphological organisation (cf.
postulate 4)--is characteristic for a given species and constitutes a barrier to
inter-species synaptonemal alignment and, hence, to the fertility of hybrids.
Topology of growth, direction in space and number of sequential cellular
divisions are directly or indirectly based on the quantitative and qualitative
specificity of the DNA:matrix-protein interaction; a cellular clone of a
definitive line will thus have the potentiality to fill a given morphologically
defined volume; these mechanisms are modulated by cell to cell interaction
involving extracellular matrix elements.
Available sites on the DNA must be satisfied by a corresponding number of
specific matrix components; the programmed imbalance of this relation
leads to DNA replication and cell division.
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Scherrer
(10) Any unprogrammed and imbalanced perturbation of the DNA-matrix or
RNA-matrix interactions leads to the disruption of programs of temporal
and spatial gene expression, of growth control and morphogenesis.
THE BASIC MECHANISMS
The basic postulate of the matrix hypothesis is that the "extra-genic",
non-protein-coding D N A has a directing function in the organisation of the static
and dynamic architecture of the cell, which partially conditions its phenotypic
function. At each step of differentiation partially different fractions of the D N A
are thought to be involved. The D N A carrying genes for specific cell function
would hence also influence spatial organisation and morphology; quite obviously,
the latter must be adapted to cell function. Indeed, there is a logic in an
arrangement which will link genetically cell-specific gene expression with the
blueprint of the infrastructure necessary to support both, the mechanism and
control of the expression of those genes and the execution of their phenotypic
function.
The postulate of a direct action of the nuclear D N A in the cell's architecture
meets a quite obvious and trivial difficulty in the compartmentalisation of the
eukaryotic cell: we see the cell basically as a dual architectural entity, composed
of nucleus and cytoplasm. But typically, stem cells or differentiation-arrested cells
(as resting lymphocytes), have minimal cytoplasm. Furthermore, in most cells the
nucleus is, in fact, an ephemeral structure. Disrupted during cell division, it
cannot be part nor condition of the permanency of the cell's architecture and
organisation, which must constitute a continuum throughout interphase and
metaphase. Since the structures conditioning this architecture must be maintained
throughout cell division, at least some of the matrix networks must be faithfully
duplicated in every cell division. Indeed, centriole duplication often occurs at the
onset of the S phase, and the daughter centrioles separate only later on, moving
to opposite poles of the cell prior to morphological segregation and redistribution
of the inactivated chromosomes; then only are the new nuclei formed.
The filamental networks of the cell are hence likely to represent the only
permanent structures throughout the cell cycle which, in conjunction with the
plasma membrane skeleton, represent the permanent organisation of the cell.
This and other facts led some to consider that DNA, genes and chromosomes are
not so important as presently believed (Lima de Faria, 1983), and that the
continuity of the cell is largely given by some non-genic mechanisms based on the
self-assembling potential of living matter. What then is the basis of the opposite
idea: that DNA may govern directly, and not only through gene expression and
the assembly of its products, the matrix organisation?
We may consider the cell as a unit space to be filled by a three dimensional
network. The question arises how, within this network, positions and interconnections are defined according to the function of specific cellular sectors or
transport channels, feeding specific information to the sites o f phenotypic
expression and function (cf. e.g. Lawrence and Singer, 1986).
UnifiedMatrix Hypothesis
163
Data arising over the past ten years demonstrate with increasing strength that
the cell is highly sectorized, not only morphologically but also in respect to
localisation of DNA and (pre-)mRNA. The old observation that in normally
differentiating cells nucleoli occupy specific positions is being complemented by
the recent finding of Manuelidis (1982, 1984a, 1985) showing that satellite DNA
and centromeres occupy specific topological positions. Interphase chromosomes
seem to occupy specific sectors (Ellison and Howard, 1981; Gruenbaum et al.,
1984), and specific chromosome segments occupy specific topological positions in
the nucleus (Hens et al., 1983). The topology of centromere and hence of the
position of specific chromosomal segments seems to change in differentiation
(Manuelidis, 1985).
Even more to the point are the experiments showing by in situ hybridization
of specific repetitive sequence probes that specific DNA is located in topologically
defined sectors of the nucleus, as are some specific transcripts (Lifschitz et al.,
1983). Such data are complemented by the fact that newly induced or cell-specific
proteins and their mRNA appear in delimited sectors of the cytoplasm and, that
hence, proteins are not synthesized randomly all over the cell (Lawrence and
Singer, 1986; Colman et al., 1982; Kuhlmann et al., 1975, see also below). All
these data tend to show that the (unmanipulated!) cell has a highly specific
static and dynamic architecture and functional organisation. Our challenge is
hence to try to understand the molecular basis of such an organisation in which,
almost inevitably, the filamenteous networks will play a crucial role. Indeed, the
DNA, pre-mRNA and mRNA, as well as the polyribosomes, are long known to
be attached to nuclear and cytoplasmic matrix or skeleton (Maundrell et al.,
1981, and references therein).
From a theoretical standpoint, the cell's basic structure is thus to be
understood as a three-dimensional network or lattice in which every position is
defined. Since this model concerns a living cell, and not the steel skeleton of a
building, this lattice has to be dynamic and not merely static: lines of defined
positions have to form vectors of functional interconnection and of dynamic
change. In a regular lattice involving straight lines at right angles (Fig. 1A), every
point in space is defined by three coordinates, e.g. X10, Y10, Z10, or in the
general case by three types of "redundant signals": Xn, Yn, Zn. In turn, such a
lattice can be reconstituted by assembling multiple straight segments of given
length, e.g. Xa-Xb, Ya-Yb, Z a - Z b , Xb-Xc, etc. Clearly however, as in
geometry the triangle is defined by the length of its sides, any kind of irregular
three-dimensional network can also be built on this basis, provided there exists
a combination of redundant signals placed at specific distance which define
unequivocally the points of contact of the variably shaped fibres constituting the
network (Fig. 1A: the length of a, b, c, etc. define the points A, B, C, etc.).
Applied to biology, the problem is thus to propose mechanisms which allow
construction of a three-dimensional matrix, by which the cell could be sectorized
(Figure 1B) and in which given genes could occupy specific positions (e.g. a, bc,
cbb, etc., in Fig. 1B) and where, furthermore, the gene products, RNA and
protein, would be generated and transported along specific vector channels
(arrows from cbb, dda, etc, in Fig. 1B).
164
Scherrer
A
I
;A\
B
Fig. 1. Shape and sectorisation of the unit cell. (A) Example of a topological lattice. In a
three-dimensional lattice, placed within a perpendicular system of coordinates, every point is
determined by the value of the coordinates X, Y and Z. If the points of intersection (Xm, Yn, Zo) are
sites of specific interaction then, the length of junction (x, y, z) in between individual points will define
the topological position of every point, and hence the organisation of the overall network. If the
length of individual junctions varies (a, b, c, etc), then any kind of three-dimensional shape and
internal organisation can be created (lower panel). A system combining specificity of sites of
intersection and distance in between them contains topological, morphogenic and organisational
information. (B) The sectorisation of the cell. Based on the principles shown in Fig. 1A, the sites of
DNA-matrix-DNA interaction and their relative distance in the DNA define a three-dimensional
network (cf. Fig. 2C) liable to determine the shape and internal organisation not only of the nucleus
but also of the entire cell. The schematic representation is meant to show an undifferentiated cell
whi~ch,most often, has minimal cytoplasm, as is the case of early precursor cells in differentiation (e.g.
hemopoietic stem cells), resting cells (lymphocytes), and de-differentiating cells (cytoplasmic shedding
of iris cells in lens regeneration, etc). In such a system, every DNA segment and every gene will be
placed in a specific sector of the nucleus (a, ab, aab, etc), and specific messages and controlling factors
can be sent into specific sectors of the cytoplasm. Examples of specific localisation of genes, of specific
mRNA and RNP are discussed in the text.
A t this p o i n t of o u r discussion the c e n t r a l p r o p o s i t i o n of the M a t r i x
H y p o t h e s i s i n t e r v e n e s : that it is the D N A itself which directs the overall
o r g a n i s a t i o n of the t h r e e - d i m e n s i o n a l n e t w o r k of cellular filaments, a n d that the
transcripts, i.e. the p r i m a r y a n d s e c o n d a r y p r e - m R N A , recognize a n d e x t e n d in a
d y n a m i c fashion this k i n d of o r g a n i s a t i o n . I n o t h e r words, the f r a c t i o n of the
t r a n s c r i b e d a n d u n t r a n s c r i b e d D N A t a k i n g part n e i t h e r directly n o r i n d i r e c t l y in
UnifiedMatrix Hypothesis
165
protein synthesis, is thought to contain in inventory of pleiotropic signals which,
in given specific combinations, can be recognized by specific proteins (Fig. 2A
and B). By interacting with specific DNA sequences and in between themselves,
these define specific points of the matrix where the DNA of different domains
join each other (Fig. 2C). From such "roots", the further assembly of the
filamentous network could be completed, possibly by self-assembly of fiber
oroteins (Fig. 3).
In other words: DNA, and possibly pre-mRNA which share specific snRNA
with the matrix structures (Maundrell et aL, 1981; and references therein), would
directly constitute building templates for the organised assembly of the static and
dynamic parts of networks which, once constituted, would in turn provide static
and dynamic recognition points for specific segments of the nucleic acids. Since
the DNA signals directing this assembly are thought to be of pleiotropic nature, a
three-dimensional lattice would result (Fig. 2C) in which segments of specific
DNA from the same or different chromosomes would interact directly or
indirectly. As a result, any segment of the DNA taking part in this system would
find itself in precise positions in the lattice and hence in specific sectors of nucleus
and cell (Fig. 1B). Figures 1 and 2 and their legends formulate and illustrate these
basic propositions in more detail.
Secondarily, the combination of proteins interacting with thus defined
positions of the DNA are thought to assemble into an organised filamentous
network of its own which, once constituted, might become temporarily independent of its nucleic acid building templates (Fig. 3). This is the case in mitosis (Fig.
3C); the reconstitution of the daughter cell nuclei would consist in part of the
reinsertion of the DNA segments, temporarily fixed to the scaffold of the mitotic
chromosome (Earnshaw and Laemmli, 1983), into their assigned positions within
the matrix. In every cell division, according to the fraction of DNA involved (i.e.
the euchromatic part of chromatin), the decision to maintain or alter this
organisation might constitute a basic event of cell differentiation (Fig. 4)
corresponding possibly to the events of "Quantal mitosis" postulated by Holtzer
(1972). In this fashion the seemingly conflicting postulates of the apparent
non-genic permanency of the cells architecture and its dependency on the genetic
apparatus of cell and species, as well as its modification in the course of
differentiation (cf. Manuelidis et al., 1985) might be reconciled.
Some of the basic implications of this model seem to correlate reasonably
well with present knowledge about nucleic acids and cellular matrix. Being
pleiotropic, most of the putative signals at the contact points would have to
correspond to repetitive DNA sequences, and the matrix structures would have to
include a quite extensive but defined population of proteins (cf. Fey et al., 1984).
In fact, as in the case of the non-histone proteins, a n d o f the pre-mRNP, mRNP
and prosomal "recognition" proteins (Vincent et al., 1983; Martins de Sa et al.,
1986), thought to control gene expression, we are confronted here again with the
properties of a multikey system of pleotropic signals (discussed e.g. within the
Cascade Regulation Scheme; Scherrer, 1980). These are of fundamental theoretical necessity in any kind of biological (and other) system of control of
information. In the case discussed here, the system would have the additional
166
Scherrer
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) l~l l 11~ - ~~ l' T1 1l ~~' 11 ~'~
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Fig. 2. The basic mechanisms. (A) The site-specific DNA-Matrix-DNA interaction. The DNA
contains signals (labelled a, b, c, etc.) specifying interaction with specific proteins or their complexes.
These (matrix) proteins (labelled A, B, C, etc.) interact at such sites with the DNA on the one hand,
and between themselves on the other. (Alternatively, the single proteins (A, B, etc.) could contain
multiple sites of specific interaction with several adjacent signals in the DNA). In a second step, the
site-specific (matrix-) proteins are thought to be joined by other polymerisation-prone proteins
forming altogether the matrix network (dotted area). The specific sites in the DNA will hence
simultaneously direct the organisation of the matrix and the specificity of interaction of specific DNA
segments, situated in the same or in different chromosomes. The specific DNA sequences containing
these signals will hence be repetitive to various degrees, and the proteins will only be partly specific to
a given DNA domain. (B) A code of DNA-matrix protein interaction. The specificity of the
DNA-matrix-DNA interaction is thought to be based on the combination of recognition signals (a, b,
etc.) for specific proteins, e.g. abe, bx, adn, etc. Such a system would have to be governed by a
"code" controlling the combination of signals which allows it to operate with relatively few pleiotropic
recognition factors (matrix proteins). The about 105-106 transcriptional units in higher eukaryotes
could hence be organized into a three-dimensional network by a few hundred matrix proteins. (C)
The creation of the DNA matrix network. When interaction takes place, the linear arrangement in
the chromosomes (A, B, C and D) of sites of DNA-matrix-DNA interaction is transformed into a
three-dimensional network of individual chromatin domains (A1-A8, etc.); these are thought to
interact at specific sites. Such sites placed at relatively short distances will define the domains; placed
within these domains they may interact with the corresponding distal loci on the same or on other
chromosomes. In consequence, every DNA segment will occupy a specific topological domain of the
nucleus and the whole system will be linked throughout. In the right hand panel, the theoretical
maximal extension of the network is shown: this virtual network of interacting sites is thought to be
modulated and reduced in specific types of differentiated ceils (el_ Figs 3 and 4). Quite evidently this
very primitive schematic representation is thought to be much more complex; in particular not every
DNA domain will necessarily be attached to the nuclear lamina, but may be fixed to an inner scaffold.
Furthermore, if for "graphic" reasons a systematic representation of the DNA domains in the form of
loops was chosen, these should not a priori be confounded with the basic loops of chromatin
organisation (Cook et aL, 1976; Paulson and Laemmli, 1977; Vogelstein et al., 1980).
Unified Matrix Hypothesis
167
~D ~ A .
C
A
~
AB
B
B
,lh
C
Fig. 3, Formation of the matrix network and its maintenance throughout interphase and metaphase.
(A) The linear organisation of the four chromosomes (A, B, C, D) shown here with their sites of
potential specific DNA-matrix-DNA interaction (black dots) having specific positions a(n), b(n), c(n)
or d(n) in the DNA, each one loaded with specific (pleiotropie) factors, represents the first degree of
organisation of the network. Some domains (e.g, A1, 2) are in decondensed chromatin, others remain
in condensed ("heterocbromatic") state (e,g. A3). (B) Interaction takes place in a site-specific manner
(e.g. in between sites ax and dy, cm and bn, etc.) under the control of the signals and factors bound to
each site and possibly, to centromeres and telomeres (open rings): a three dimensional network is
created in which every position is determined by the pleiotropic signals and factors common to
interacting sites. From these sites of interacting constituting "roots" of polymerisation, the matrix
network is formed which is conditioned, thus, by the interaction at the bases of and in between sites in
the domains of the fraction of DNA in decondensed chromatin. In this picture, the basis of the loops
are placed at the lamina and hence at the nuclear envelope; quite obviously, not every DNA loop
needs to sit at the lamina. In the course of differentiation, the nuclear envelopt~ is thought to retract
from the periphery of the cell leaving some matrix elements behind in the cytoplasm. (C) The cell has
gone through mitosis and the (interconnected) mitotic chromosomes will start to decondense
according to panel (A) into chromatin domains, which will be re-inserted at their specific sites into the
matrix network (B). In differentiation, additional loops may however form, conditioning new sectors
of matrix, and the chromatin of other domains may become heterochromatic, leading to the loss of
the corresponding matrix sectors (cf. Fig. 4).
p o t e n t i a l c a p a c i t y to o r g a n i s e t h e D N A into an a r c h i t e c t u r e in w h i c h g i v e n g e n e s
w o u l d r e s i d e in specific l o c a t i o n s ( w h e r e d i f f e r e n t ) , a n d in t h e D N A , u n l i n k e d
genes c o u l d b e t e m p o r a r i l y l i n k e d , c o n s t i t u t i n g c e n t e r s o f c o o p e r a t i v e action.
F r o m t h e r e , g e n e p r o d u c t s c o u l d b e d e l i v e r e d to specific t r a n s p o r t a n d e x p r e s s i o n
c h a n n e l s l e a d i n g to specific s e c t o r s o f t h e c y t o p l a s m , t h u s c o n d i t i o n i n g t h e
p h e n o t y p e . This a r c h i t e c t u r e w o u l d also define t h e o v e r a l l m o r p h o l o g y a n d size
o f t h e cell a n d , s e c o n d a r i l y , t h a t o f s u p r a - c e l l u l a r c o m p o u n d s a n d o r g a n s .
168
Scherrer
D
A
D
A
!
A
B
Fig, 4. Modulation and reorganisation of the matrix network in differentiation. The basic
distribution of specific DNA domains into sectors of the matrix is thought to be complemented by a
variable network conditioned by the activation or inactivation (i.e. decondensation and condensation)
of specific cfiromatin domains (loops). In consequence, to accommodate changes in cell function, the
matrix network will be modified in crucial steps of differentiation (which might correspond to those of
"Quantal Mitosis" (Holzer, 1972)). This variable network could also specify the points of
DNA-matrix-pre-mRNA interaction influencing, according to the state of differentiation, the
differential processing and sector-specific transport of (pre-)mRNA. Quite obviously, the participation
of the chromatin segments of one or the other of the allelic chromatids could also matter in such a
system (e.g. the rearranged or germ-line alleles of an immunoglobulin gene).
EXPERIMENTAL CORRELATIONS A N D THEORETICAL
EXTRAPOLATION
Interdependence of D N A Mass and Organisation with Cell Architecture and
Generation Time
The postulate that DNA content conditions the size of a cell--its main
architectural feature--was proposed years ago by Cavalier-Smith (1978); the
matrix hypothesis, among other propositions, adds site-specificity and an interdependent protein matrix to this DNA network. As shown in Fig. 5A, the
haploid DNA content shows a linear correlation when plotted versus cell volume
(Commoner, 1964). In addition, we have to keep in mind that selection in
evolution acts on the phenotype exclusively and that the DNA as the archive of
the cell's blueprints has to simultaneously provide for the emergence of
modification as well as for the capacity to integrate new solutions of functional
necessity without changing the basic patterns of the plan.
The matrix hypothesis (postulates 1 and 3) may allow for a rational
interpretation of the correlation of cell volume and DNA content and proposes,
furthermore, a novel explanation to the still mysterious fragmentation of many
genes into separate exons at DNA level (Fig. 5B). Where the DNA is part of a
specific three-dimensional network as a building plan for, for example, an
erythroblast, and if in evolution such a cell and its nucleus grow bigger in some
species, then to maintain this organised network spanning the nucleus and
integrating the specific genes and gene fragments expressed in this cell, the DNA
must expand itself. Since the points of interaction are fixed, the only solution is to
intercalate more and more spacer DNA in between genes and, possibly, gene
Unified Matrix Hypothesis
169
~a
~"~
10010/
I
102
I
I
I I I
I
103
104 p3
Cell Volume
Fig. 5. Correlation of cell volume with DNA mass and its possible impact on internal DNA
organisation. (A) The DNA content correlates with cell volume. Relationship between cell size of
erythrocytes of various vertebrate genera and the organism's characteristic cellular DNA content
(adapted from: Commonor, 1964). (B) The generation of extragenic and intragenic (intron-type)
spacer DNA. If the DNA is interlinked into a three-dimensional network of functional significance, in
order to maintain the overall topology and sectorisation of nucleus and cell and to keep a given gene
or gene fragment (exon) at its assigned spot, the total mass and individual DNA length has to vary
when the volume of the cell changes under selective evolutionary pressure. Since the protein-coding
DNA (and correlative information necessary for control of pre-mRNA processing, transport and
translation of the mRNA) remains more or less constant between phenotypically related species,
spacer DNA has to be intercalated in between genes in a gene cluster, and in between exons of an
individual gene. This process may have led to the dispersion of genes within a cluster, and to the
fragmentation of the gene and its dispersion at DNA level.
domains (exons). If the D N A is in addition directly involved in specific
matrix-protein interaction, then, due to the pleiotropy of these signals, such D N A
will be repetitive in sequence (e.g. the D N A linking the c h r o m o s o m e domains in
Fig. 5B). Cellular volume and D N A mass will thus grow in concert, but the
blue-print of organisation, the genes and, to a first approximation, the D N A
complexity, will remain stable.
The second correlation, that relating D N A content to generation time, is less
straightforward to interpret: in relation to cell mass and biochemical potential,
the amount of D N A to be synthesized is negligible in an ordinary cell. If however
D N A synthesis is a process highly organised in time a n d space, which must be
interrelated and coordinated with the simultaneous synthesis of a copy of the
matrix network of the daughter cell, then this observation starts to m a k e sense.
The separation of the daughter cell's centrioles at the end of S phase, having been
synthesized at its onset, and their m o v e m e n t to opposite poles of the cell could be
interpreted as the beginning of the disengagement of the daughter cells matrix
networks. If the metaphase c h r o m o s o m e s are drawn by specific spindle fibers
attached to individual kinetochores (constituted in yeast by specific AT-rich D N A
sequences; B l o o m et al., 1982; Carbon and Clarke, 1984) into specific sectors of
the future cell and nucleus, then the D N A could be unfolded and resuspended
back into specific positions of the network of which it was the original template.
In this fashion might be a c c o m m o d a t e d the seemingly conflicting postulates of the
apparent non-genic p e r m a n a n c y of the cell's architecture and its dependency on
the genetic apparatus of cell and species.
170
Scherrer
Transient Linkage of D N A Domains of Different Chromosomes
Proceeding to more specific architectural features of the network proposed,
we have already mentioned that the inter-connection of specific DNA segments
has the potentiality to assign every gene to a specific sector of cell and nucleus.
The phenomenon of ectopic pairing in polytene chromosomes in Drosophila (cf.
e.g. Kaufman et al., 1948), linking specific interbands within (Fig. 6B) and in
between (Fig. 6A) chromosomes and with nucleoli (Ananiev et al., 1981), gives a
quite precise "macroscopical" image of the existence of this type of mechanism
(cf. review in Lima de Faria, 1983). Ectopic pairing (Fig. 6) is also visible in
between metaphase chromosomes (Du Praw et al., 1970), which occupy, obeying
specific rules, precise positions relative to each other in the metaphase plates
(Bennett, 1982). Furthermore, paternal and maternal chromosome sets remain
linked at least through the first 3 cell divisions after fertilisation (Odartschenko
and Keneklis, 1973).
There is hence ample evidence for specific interconnection of chromosomes
in interphase and metaphase. The contribution of the matrix hypothesis is to
propose that this kind of mechanism goes straight down to the individual unit of
chromosome architecture and function in interphase and metaphase: the equivalents of the polytene chromosome band and of the units of transcription and
replication, which are thought to be interconnected in between themselves and
with the matrix.
Furthermore, we may consider that the phenomena of chromosome translocation and gene transposition (review in McClintock, 1984) may reveal the
existence of such types of linkage. Indeed, positions of ectopic pairing seem to
correlate with locations of repetitive sequences generated, possibly, by transposition (Ananiev et al, 1978). The intragenic chromosome translocation in leukemic
cells (e.g. Manolova et al., 1979) may be the result of a pathology in which
dynamically linked gene fragments escape the controls that keep them separate,
and which permeate accidentally by DNA recombination a temporary and
functionally conditioned association. Indeed, gene transposition and such translocations suggest that the chromosome domains and genes involved are at least
sometimes in close molecular contact with each other. Such events may thus not
occur by chance but may be conditioned by organisation and function of cell and
genome. Along the same lines of deduction, the strange fact of the existence of
mRNAs which are encoded on two distinct chromosomes, one contributing the 5'
part and the other the 3' end (Guyaux, 1985), finds a plausible explanation,
assuming that the RNA polymerase is liable to "jump" at the site of specific
transient interconnection from the DNA of one chromosome to that of the other.
Finally, this transient inter-connection might also provide a mechanism for the
exchange of gene fragments (exons) in between functionally related genes and
thus for the emergence, based on the differential assembly of exons, of alternative
mRNAs in differentiation, and of that of new genes in evolution.
Correlation of Chromosome Organisation and Cellular Sectorisation
Another postulate which divided and still divides Molecular and Classical
Biologists, is that of the "Chromosome Field" (cf. remarks of F. Crick in Lima de
Unified Matrix Hypothesis
171
A
Fig. 6. The supra-chromosomal DNA organisation and ectopic pairing. Ectopic pairing in between
and within Drosophila chromosomes illustrates the specificity of inter-connection of chromosome
domains in interphase, and prefigures the putative DNA-matrix network. Chromosomes obey a
specific spatial organisation, e.g. in Drosophila (Gruenbaum et al. 1984). According to the Matrix
Hypothesis, this type of organisation, based on direct or semi-direct interaction of sites in between
and within chromosomes could exist in any cell. (A) Ectopic pairing in between Drosophila polytene
chromosomes of the salivary gland (line-drawing after an original micrograph by Ananiev et al.,
1981). Plain arrows: examples of ectopic pairing; open arrows: telomeric pairing; No: nucleolus. (B)
Mapping of sites of ectopic pairing in a Drosophila chromosome (adapted from Kaufmann et al.,
1948).
172
Scherrer
Faria, 1979). It is based on the observation that in related species, some specific
genes reside in specific relative positions of the individual chromosome arms in
relation to centromeres and telomeres, and to each other (Fig. 7A/B). When
multiple chromosome arms, of several related species carrying, e.g. ribosomal
genes, are arranged in parallel on a X / Y system of coordinates, with their
centromeres on the ordinate and the telomeres on a line at a 45 ~ angle (Lima de
Faria, 1980), the specific gene is always found in the same relative position on the
chromosome within a specific "Chromosome Field". This has been interpreted as
the result of an internal structural constraint originating from the centromere and
organizing the sequential insertion of specific genes into the chromosome; an
explanation hardly acceptable to the molecule-minded biologist.
The matrix hypothesis offers another explanation of this phenomenon:
indeed, if under selective pressure the cell is functionally sectorized and this
sectorisation depends genetically on the D N A , then classical evolutionary
A
0
I
ff--2
_|oA
_3
O
C
5
6
0
2
1
3
/,
microns
0
B
I
I.
J
F,*
2 ~
m
3
o
l
2
3
microns
Fig. 7. Interpretation of the phenomenon of the Chromosome Field. The "Chromosome Field" is a
concept proposed by Lima de Faria (1980) based on the facts shown in panels (A) and (B): specific
types of genes (e.g. ribosomal genes) are found in related species, most often in specific positions
relative to centromere and telomeres on the chromosome, independent of the size of the individual
chromosome arm. This fact never provided a satisfactory explanation to the Molecular Biologist. (A)
Location of the genes for 28S and 18S ribosomal RNA in 116 species of the genus Crepus
(Compositae). Note that only a few values deviate from the straight line formed by these DNA
sequences. The ribosomal genes are located near the telomeres and form a line parallel to them: they
are "telons" (adapted from Lima de Faria, 1980). (B) Location of ribosomal RNA genes in three
species of mammals: Human, gorilla and guinea pig. The "telon" distribution is of the same type as in
plants and other animal groups (adapted from Lima de Faria, 1980). (C) Possible interpretation
according to the Matrix Hypothesis: If for structural and functional reasons there is a selective
pressure in evolution to keep specific genes in specific topological sectors of nucleus and cell (dotted
area) then, by the mechanisms postulated within the frame of the matrix hypothesis, they have to be
placed in topologically specific DNA segments of the various chromosomes; in this manner the
position of e.g. the nucleolus might be defined (cf. panel A and B).
Unified Matrix Hypothesis
173
mechanisms will keep specific genes at their specific localisation in relation to
each other, and in their sequential order on the chromosomes (Fig. 7C).
Furthermore, for the kind of mechanism proposed within the Matrix
Hypothesis, it will not matter into how many chromosomes the D N A will be
divided, only the relative order of genes and other structural D N A segments will
be important, but not the chromosome number per se. (The 6 chromosomes of
Muntjacus Muntjak or the 46 of Muntjak Reevesi will be able to condition an
almost identical phenotype; cf. Lima de Faria, 1980). Indeed, according to the
matrix hypothesis, the basic mechanism of cellular sectorisation and D N A
organisation implies simply permanent and dynamic matrix attachment points,
placed at given distances and in a given sequential order along the DNA,
conditioning the organisation of structure and expression of genome and
phenotype. That this sequential order of genes is punctuated by centromeres,
telomeres or simply by constitutive heterochromatin, and that there may be one
or many spindle fiber attachment points (cf. "diffuse centromeres" in Lagowski et
al., 1973) along the chromosome, are details of chromosome mechanics,
superimposed on the basic features of long range D N A organisation.
A Novel Type of Genetic Information: the Code and Topology of Signals
Controlling Chromosome Architecture and Matrix Organisation
It is important to notice that, within the framework of the genome
organisation proposed by the matrix hypothesis, topological positions of signals
and their mere distance in the D N A start to matter. Nucleotide numbers alone
(never mind their sequence!) between two signals will amount to specific genetic
information. Two novel types of genetic information must thus be postulated, in
addition to the genetic code of protein assembly: (1) a code of pleotropic signals
defining the specificity of DNA-matrix interaction and (2) the topology of these
sites of DNA-matrix interaction, given by the distance in the D N A of the
corresponding signals and their sequential arrangement.
The precise nucleotide sequences separating at stringent distance such
encoded signals will not mattdr; they must of course obey certain general rules of
DNA and chromatin structure and may possibly carry information of classical or
novel types. Nevertheless, since mere distance will amount to genetic information, the necessity arises to postulate the existence of space filling DNA, in order
to satisfy the topological constraints discussed. In contrast to the protein coding
DNA, such sequences might be subject to frequent variation and modification
relating eventually to the individual somatic cell and organism. Quite evidently,
satellite type D N A built of repetitive sequences is a good candidate to have arisen
by such a process and to satisfy this kind of necessity. (As an example one might
mention the old enigma of the maintenance of absolute mitochondrial D N A
length in some of the petit mutants of yeast, where many or all genes are deleted
and replaced by AT-rich D N A (Bernardi, 1979)).
Quite in general, repetitive non-protein-coding D N A sequences may arise by
two types of mechanism: (1) the necessity of identical function at different
genomic sites might dictate the multiplication of a D N A sequence placed at
174
Scherrer
distant sites, corresponding to the "amplification" of a sequence motif at genome
level; (2) since all organised contiguous structure is repetitive in one, two or three
dimensions, producing actual or virtual filaments, sheets or volumes, any skeletal
element being part of (or the template for) a filament will itself be repetitive: this
is amplification in series or "magnification". Although these two types of
mechanism lead to the same result, namely the repetition of a sequence motif,
they should not be confused since they have different potentialities. At genome
level, the first mechanism might equate to medium repetitive sequences with the
potentiality of being part of one of the various systems of pleiotropic signals of
control, whereas the second might correspond to the single sequence type
characteristic for satellite DNA.
Both types of repetitive non-coding sequences may play a role within the
mechanisms proposed by the Unified Matrix Hypothesis. As just discussed, the
second type of amplification (magnification), in its potential spacer function, may
carry genetic information of the novel type. The first type of amplification
corresponds to more classical functions: the rules of signal-pleiotropy at DNA,
pre-mRNA and mRNA level, thought to exist among the non-histone proteins,
the acidic pre-mRNP protein, the mRNP and prosomal proteins (cf. Vincent et
al., 1981; Martins de Sa et al., 1986) which all call for the existence of medium
repetitive sequences at DNA level. The matrix hypothesis postulates the
existence of just another system of the same type, conditioning the DNA-matrix
and RNA-matrix interactions in both directions, i.e. the nucleic acid-protein and
the protein-nucleic acid direction. Such DNA signals, under an evolutionary
pressure different from that operating within the protein coding system, are likely
to be most often (but not exclusively), localised in the spacer regions outside the
coding sequences; in other terms in DNA segments "linking" the domains of
gene families or of individual genes, and possibly of gene fragments (exons)
corresponding to domains of phenotypic expression. The proteins corresponding
to this population of matrix proteins could count in the hundreds as shown by
Penman's group (Fey et al., 1984); classical matrix research has focussed on only
a few of them, as vimentin, desmin or other (mainly lamina) proteins, or on the
poly(A) binding protein which is a common constituent of matrix, pre-mRNP and
mRNP complexes (Maundrell et al., 1983).
It is evident that if such proteins were to be organised into the building
blocks of the matrix, giving specificity within the network of otherwise selfassembling filaments, a specific code must exist at DNA level composed of a
combination of signals (cf. Fig. 2B) recognised by these proteins, either directly
or through the bias of the RNA part of SnRNP, ScRNP and the Prosome
complexes which are constituents of the nuclear matrix and the cytoskeleton (Pal
et al., 1988; Grossi de Sa et al., 1988). The nature of such signals in the DNA is at
present unknown; the recent data of Laemmli's (Mirkovitch et al., 1984) and our
group (Razin et al., 1985; Scherrer and Moreau, 1985) on the matrix attachment
of specific gene domains tend to indicate that At-rich and repetitive DNA
elements are involved.
It is evident that the type of DNA assigned to the morphogenic functions
postulated will obey different rules in regard to effects of mutation, deletion and
UnifiedMatrix Hypothesis
175
evolution, compared to the protein-coding parts of the genome. Furthermore, the
chromosome morphology, in as far as it reveals gross features of this virtual
organisation, will partially reflect a latent image related to the phenotype. This
organisation might be reflected in the banding pattern of chromosomes which
characterize a species, but also relate different species to each other (Seth et al.,
1976). Indeed, the fusion of the 46 telomeric chromosomes of Mus Musculus into
the 23 metacentric chromosomes of Mus Posciavino (Capanna et al., 1976) will
still produce a mouse, albeit of a different size. The inversion of a chromosome
arm conserving its banding pattern correlates, however, with the physiological
difference between Man and Chimpanzee, which differ in their morphology and
the building plan of their nervous system although sharing an identical hemoglobin. Structural genes and gross chromosome patterns are thus maintained, but
details of the overall chromosome and local DNA organisation may change.
Interdependance of Cellular and Genome Organisafion, and the Separation of
Species in Evolution
Having established this scheme of defined long range DNA organisation and
topology, several further implications become apparent. We may mention in
particular those concerning the mechanisms of meiotic crossing over and somatic
sister chromatid exchange. Legitimate and/or illegitimate recombination implies
that the sister chromatids align physically (along the whole chromatid in meiosis
and locally in sister chromatid exchange), and have the possibility to interact at
precise positions which must be localised in extragenic or possibly intragenic
(introns) spacers. In Drosophila, the units of meiotic complementation correspond grossly to the polytene chromosome band (Judd et al., 1972), and
although intra-band and intra-coding sequence recombination occurs (e.g. in
genic conversion), apparently it occurs at lower frequency (per cell division)
compared to meiotic recombination. As the examples of accidental aberrant
crossing over show, intra-genically [e.g. in the cases of the hemoglobin Lepore
deletion (Chabloune and Verdier, 1983), or in the chromosome translocation
associated with Burkitts lymphoma (Manolova et al., 1979; Klein, 1981)], or
extragenicall~ [in the cases of the yeast "Petite" mutation (Bernardi, 1979)],
aberrant recombination may lead to disaster for cell and organism. The point to
point alignment of the chromatids in the synaptonemal complex implies,
however, that the genes and gene fragments to be exchanged are in precise
positions when recombination occurs: again topology, i.e. relative DNA distance
matters, to fix and maintain the pattern of signals conditioning this alignment
(Fig. 8).
We may touch here on the rules of the molecular basis of speciation. Indeed,
the mule or hinny living happily with the genes of two different species cannot
reproduce since horse and donkey sister chromatids cannot align properly: they
are lysed instead of forming a healthy synaptoriemal complex (Chandley et al.,
1974). On the other hand, chromatids of related genomes having different DNA
content can form a functional synaptonemal complex by maintaining the pattern
Scherrer
176
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<SY
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II ! 1
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i)
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<SY
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9
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=
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N her'
E
Fig. 8. Correlation of topological organisation in phenotype and genotype and the species barrier.
(I) Topology of cell sectors and gene alignment in chromosomes. The specificity of DNA-matrix-DNA
interaction conditioning the topological and functional organisation and sectorisation of nucleus and
cell (panel A, A') entails the sequential order of gene domains (e.g. a, b) in the chromosomes (e.g.
chromosomes N and N'), as shown by the Chromosome Field (cf. Fig. 7). Phenotypic pressure
exerted at the level of topological constraints in cell function will thus bear directly on chromosome
organisation. The chromosome architecture will represent (e.g. in its banding pattern) a first blueprint
of organisation of the specific organism, which is characteristic of every species. Represented is the
case of cells of different size (A, A') of two related species which are thought to be able to form fertile
interspecies hybrids (Rees et al., 1982). (If) The specificity of the pattern of sites involved in meiotic
recombination and sister chromatid exchange may constitute the species barrier. (A-E) In meiotic
recombination and in sister chromatid exchange the paternal and maternal genetic information has to
be exchanged productively; this is done, e.g. in meiosis, by alignment of the two allelic chromatids
(panel B) within the synaptonemal complex (panel C). The "macroscopical" alignment of the
chromosomes is thought to be maintained right down to the molecular level. To allow for correct
alignment and pairing, the linear arrangement of genes has to be kept identical between the DNA of
allelic chromosomes (N); in order to allow for single strand crossing-over at "hot-spots" placed
logically in between genes and gene domains (panel C, arrowheads), the localisation of these potential
sites of recombination has to be rigorously identical. If this alignment of genes and "hot-spots" of
crossing-over is changed under phenotypic pressure (as that thought to separate species) then the two
heterogeneous chromatids (N, Nhet) will not be able to align properly any more (panels D and E)
although the two genes within the domain are identical. This happens, indeed, in the abortive
synaptonemal complexes of infertile interspecies hybrids, e.g. in the mule and hinny (Chandley,
1974). Phenotypic pressure leads, thus, via cellular and genome organisation, and by the mechanism
inherent in sexuality, to the separation of species; these mechanisms may also explain why new species
emerge rarely and most likely from homozygous clones - - ( A ' - C ' ) . If, however, only the size of the
cell changes whilst its sectorial organisation remains identical (panel A'), then meiotic recombination
may still take place: simply the "spacer" DNA (open arrows) relating to mere cell size is excluded
from the synaptonemal complex (panels B' and C'); this is the case in the fertile interspecies hybrids
of some plants, e.g. of SecMe species (according to a proposition of Rees et al., 1982).
UnifiedMatrix Hypothesis
177
of synaptonemal alignment, but excluding some of the mere spacer DNA (Rees et
al., 1982).
The evolutionary pressure driving a phenotype to adopt to its ecological
niche by the sectorial organisation of the DNA and matrix networks (cf. above
and Fig. 7) will hence lead to genetic separation of the successful variant if, by the
mechanism of the unified matrix hypothesis proposed, phenotype and genotype,
i.e. morphology and chromosome organisation, are directly interdependent, and
not only through the bias of peptides which can be shared by widely different
species.
Matrix Related Post-Transcriptional Mechanisms of Gene Expression
Proceeding to other implications we may recall that, within the Matrix
Hypothesis, the ultimate justification for a rather rigid structural and sectorial
organisation of the genomic DNA is thought to relate to the specific phenotype,
and thus to the mechanisms of gene expression which condition phenotypic
expression. In other words: genes have to cooperate (e.g. the alpha and beta
globin chains encoded on different chromosomes), and their pre-mRNA, mRNA
and protein products have to reach specific sectors of the cell by specific transfer
channels, as is most evident, e.g., in the case of myelin mRNA (Colman et al.,
1982). The basic overall organisation of cell and nucleus by the genomic DNA is
hence thought to be complemented by a more dynamic DNA-matrix interaction
in which the transcribed DNA (Smith and Berezney, 1980; Robinson et al., 1982;
Razin et al., 1985; Rzeszowska-Wolny et al., 1985) would give over the primary
transcripts at specific positions (Razin et al., 1985) to the matrix, on which RNA
processing takes place (Maundrell et al., 1983; Madman et al., 1982). Indeed
several components of pre-mRNP complexes are shared by the matrix structures,
such as the snRNA (Maudrell et al., 1981, Maxwell et al., 1981; and references
therein) and the poly(A) binding protein (Maundrell et al., 1983).
Since the very specificity of pre-mRNA processing is thought to be influenced
by differential attachment of the transcribed DNA at specific points of the matrix
(such DNA signals might operationally have the properties of "transcription"
enhancers, cf. review in Yaniv, 1984), segments of the primary mono- or
polycistronic pre-mRNA could be differentially attached and yield different
mRNA (Razin et al., 1985; Rzeszowka-Wolny et al., 1985), according to the level
of differentiation of a cell and its stage-specific matrix. DNA modifications such
as methylation, and DNA-protein interactions within chromatin could thus lead
to post-transcriptional effects at the level of the controls of processing.
Another result of such a scheme would be that different distally attached
DNA domains could temporarily cooperate within topologically defined sectors of
the network, and deliver products of distally located genes to common expression
channels. Since the operon has "exploded" in eukaryotes (exception: the viral
genomes) and quite often cooperating genes (as e.g. the subunits of hemoglobin
or other multi-component proteins) are on different chromosomes, such a
cooperation might reflect a necessity for the cell; no obvious mechanism for this
kind of cooperation has been proposed as yet. A further potentiality of such a
system is the possibility that the genes of a gene family could be expressed in
178
Scherrer
different combinations according to the status of differentiation and development
of a given cell. Mechanisms of this kind must be sought, to take into account,
e.g., the changing isozyme patterns, or the developmental expression of, e.g., the
globin genes.
At the DNA level, this mechanism again calls for pleiotropic signals and
hence repetitive DNA, localised in extragenic spacers for common genes and in
introns for highly dispersed genes subject to differential processing. Since at such
cooperatively acting points the DNA is thought to transfer the transcripts to the
processing network, the further possibility arises that such sites might serve as
entry points for proteins constituting and being involved in the DNA: matrix
interaction and which would end up at the pre-mRNP : matrix level. As a possible
example one might consider the SV40 T-antigen which has a binding site on the
viral DNA (Rio and Tjian, 1983), but the mass of which is associated with
(cellular) pre-mRNA (Khandjian et al., 1982).
If the DNA has the potential ability to organise the static and dynamic
matrix network in relation to gene expression, and in particular, if some proteins
could be transferred from DNA to RNA, then the further possibility is given that
it is the primary transcripts and successive processing intermediates that carry
out, during processing and transport, an organizing function (postulate 5).
Pre-mRNA might at the same time be template and substrate to the processing
and transport machinery, modulated by successive processing steps, extending
and supplementing in such a manner the architectural and organising function of
the DNA. This view is supported by the finding of Fey et al. (1986) that extensive
domains of the nuclear matrix collapse when transcription is arrested by drugs.
It has been obvious for a long time that the mRNA in its final form cannot
carry all the information necessary for all the collateral mechanisms involved in
its prior transport and expression; the pre-mRNA however has no limits in this
respect, and was proposed to carry in its structure the chronology of mechanistic
and regulative interventions necessary for the delivery of its genetic message (cf.
Fig. 19 in the "Cascade Regulation"; Scherrer, 1980).
The topology of the DNA:matrix-protein interaction may thus differentially
influence the processing of pre-mRNA. The latter might serve as a template for
the organisation of processing and transport channels on the matrix leading to the
cytoplasm. Finally, proteins of DNA: matrix interaction may be transferred to the
RNA and prolong this interaction at pre-mRNA level.
Morphogenesis of SupraceHular Structures and Growth Control
A further implication of the matrix hypothesis to be discussed relates to
morphogenesis of supra-cellular structures, of cellular clones and eventually
organs, and to growth control (postulates 8 and 9). Some components of the
matrix networks are known not to be limited to the individual cell but transcend
its limits. By defining supra-cellular compounds in conjunction with sequential
vectorial control of cell division, they have the potential to fill in a specific volume
of pre-defined shape. Before touching on these matters we will first have to come
back to the putative mechanisms of sectorisation in the individual cell.
Unified Matrix Hypothesis
179
If the cell is sectorized in respect to the matrix networks, by the contact
points of interaction involving specific activated D N A segments which are
conditioned by differential (possibly allelic!) activity of the chromatid sets, then
the line of subdivision of the cell, i.e. the directionality of division, starts to
matter (Fig. 9A). Quite obviously, the cell and the matrix networks can divide
strictly symmetrically, or asymmetrically to various degree. Some observations
show, indeed, a clearcut correlation between plane of cell division (conditioned
by spindle orientation) and events of differentiation occurring after a specific
number of divisions (e.g. in moss protonema formation; Johri, ' 1978). Thus, a
program of the direction and number Of consecutive cellular divisions must be
postulated in line with programs of differentiation.
The molecular mechanisms that might allow for the predetermination of the
direction of cell division are quite obviously most difficult to imagine. The
example of the moss protonema (Johri, 1978) and others in the literature however
show clearly that the orientation of the spindle, i.e. the implantation of the
centriole, in a given sector of the mother cell cytoplasm often precedes, and
~
v~
A
B
Fig. 9. Vectorial cell division in differentiation and morphogenesis. (A) Specific division relative to
cell sectors. In a system of cell sectorisation the plane of cell division will matter: the centrioles and,
hence, the daughter cell nuclei will be generated in different sectors of the permanent matrix network
maintained throughout metaphase; the sectors of re-insertion of the DNA will partially change. Since
each parental (haploid) chromosome set has a tendency to stay together in mitosis (Bennett, 1982),
symmetric or asymmetric cell division in relation to the specific matrix sectors generated by the
(allelic) DNA segments is possible. Ciearcut examples of correlation of spindle re-orientation, plane
of cell division and events of differentiation are known (Johri, 1978). In turn, the centriole
implantation and, in consequence, the orientation of the spindle could be conditioned by the
specificity of the parental matrix network; a program of cell division might thus be established. (B)
The morphogenic potential of vectorial cell division. To fill a given specific volume, a clone of cells
(e,g. those of the Drosophila wing) will have to go through a given number of cell divisions to provide
a specific cell mass. If the direction of each sequential cell division is also programmed, the cell mass
created will have a specific shape. Cell to cell interaction--where it occurs---will of course have to
modulate this system.
180
Scherrer
hence most likely determines, the plane of cell division. The postulate of
sectorisation, i.e. the segregation of the cytoplasmic information content gives
however a first hint to the very possibility of a selective centriole implantation.
Since this event leads to the positioning of the daughter cell nucleus in a specific
niche of cytoplasm with its specific informational microenvironment, the further
program of its activity could be modulated. Indeed, we reach familiar ground: the
activation of hen erythrocyte nuclei in a heterokaryon (Harris, 1970) and nuclear
transplantation experiments made us families with the specific impact of a given
cytoplasm on nuclear program (Gurdon, 1975). The clue is thus in the first place
cytoplasmic segregation which, as in the fertilised oocyte, would program the
incoming nucleus. There remains the mystery of the timing of sequential selective
centriole implantation. All the Matrix Hypothesis might provide is an organized
reference system in space, the logical material basis for selective centriole
positioning.
On the other hand, simple logic tells us that the number of cell divisions in a
clone must be programmed since the approximate final volume of a cell
compartment or an organ is predetermined. Combining the number of divisions
and their direction in space within a program, any morphological shape can be
predetermined; of course such programs will have to be modulated by cell to cell
interaction within and between cellular clones. The example of the six compartments of the Drosophila wing (Fig. 9B), separated by virtual lines partially
unrelated to anatomical features (Crick and Lawrence, 1975) demonstrates the
necessity for the existence of such programs. Since somatic mutagenesis by X-rays
leads to the local breakdown of such virtual lines (Lawrence and Struhl, 1982),
DNA must be involved directly or indirectly in their establishment and
maintenance.
The molecular mechanisms conditioning these programs are of course totally
unknown at present. Postulates 8 and 9 of the Matrix Hypothesis propose just one
possibility to imagine a solution by a molecular mechanism involving the DNA-matrix
interaction.
Postulate 9 is just the long lasting necessity of postulating molecular
countdown mechanisms. Such mechanisms could be based on the stability of
proteins or RNP complexes, but also on quantitative DNA-protein interactions.
If a given cellular clone has, for example, a once and for all heritage of 128
molecules of a given (matrix?) protein, and every haploid D N A set needs one at
a time to stabilize e.g. a given D N A loop, there is enough for 64 individual cell
divisions and no more: the loop would collapse in the sixth generation; an
analogous example implying a mechanism of negative control is obviously as easy
to conceive. Just as the few repressors of phage lambda keep the phage integrated
in the host D N A in a very sensitive quantitative balance, so a precise number of
(matrix?) proteins could keep crucial origins of replication in inactive state: their
dilution or degradation would start cell division.
We may conclude by saying that, conditioning cellular sectorisation, the
mechanism of DNA-matrix interaction has also the potential to control direction
of division. Together with a count-down mechanism determining numbers of cell
UnifiedMatrix Hypothesis
181
division, the DNA-matrix interaction might be both rigid and flexible enough to
determine numbers and direction of sequential cell divisions.
Homeostatis of Control and a Possible Pathology of the Matrix System
If the interpretations and theoretical extrapolations of experimental observation developed within the frame of the Unified Matrix Hypothesis correspond
even partially to reality, then it becomes necessary to postulate the existence of a
vast system of novel types of controls capable of regulating the DNA-matrixRNA interactions, and of adapting them to physiological needs. And correspondingly, a pattern of pathology must be thought of, that might reflect the eventual
disfunction of this system. Indeed, almost every cellular mechanism analysed thus
far in depth has found its disease, and quite often disfunction serves to probe
normal function.
A novel system of control is inherent in the very propositions of the basic
mechanisms of the DNA-matrix interaction: the recognition of specific DNA
segments by proteins (or by RNP complexes) which in turn will cooperate in the
build-up of the local and overall matrix network. We have postulated a specific
code to govern this interaction (see Fig. 2B) which, by extensive use of
pleiotropic factors, is able to keep down the energetic load to the organism of the
regulating system.
This proposition postulates thus on the one hand the existence of a family of
several hundred proteins (or RNP's) which, singly and in sets, will recognise
specific sequence signals in the DNA. The genetic apparatus of the cell must
hence provide for the presence and qualitative modulation of these regulators by
the classical pathways of protein and (polymerase III?) RNA synthesis. There is
no particular theoretical obstacle to such a proposition.
On the other hand, the corresponding signals in the DNA will obey in their
sequence variation and topological distribution the rules of molecular genetics,
and can be thought to respond to evolutive pressure according to classical
schemes and the mechanism of the matrix hypothesis. The more recently
discovered phenomena of DNA transposition, of in situ and extrachromosomal
DNA amplification, DNA re-arrangement, DNA and chromosome loss, in short,
of "genome reshuffling", will not only allow for the possible adaptation in
evolution of the genome organisation relevant to the DNA-matrix system, but
also to satisfy specific needs of a given somatic cell in differentiation. Such events,
which link genome structure to events of differentiation and morphological and
physiological adaptation are known already in the archaic Cyanobacteria (Stewart, 1985) and can therefore be thought to correspond to a biochemical system
as archaic as both the genetic code and primordial life. Thus, within the matrix
hypothesis scheme, DNA rearrangement may allow for matrix modulation and thus
for physiological and morphological adaptation in the somatic cell.
Thus far we have only considered the qualitative aspects of the putative
control system. More complex problems arise, however, when we consider the
quantitative aspects. On the DNA level, as just discussed, a limited adaptation to
182
Scherrer
the transient needs of a given cell can be thought to occur by parallel
amplification or serial magnification of specific DNA segments. These possibilities
are however relatively limited. On the other hand, there is no theoretical limit to
regulate qualitatively and quantitatively the matrix system by the protein
population and the RNP complexes known to be involved in matrix and
cytoskeletal structures. Not only is it easy to imagine variations in the types of
proteins and ImwRNA to be produced, but there is also no heresy in
considering variations in their quantitative output, and the modulation of the
activity of individual proteins by chemical or allosteric factors (hormones?), or by
"cofactors" of the lmw RNA type.
But here a conceptual problem seems to arise in conceiving such a fantastic
system of homeostatis of control governing the DNA-matrix-RNA interaction.
Nevertheless, molecular biology provides us with model cases. We know for
instance about the very precise number of repressor proteins that are necessary to
keep under control lysogeny of lambda phage, and the sensitivity of this system to
factors acting at DNA (e.g. UV irradiation) or protein (inducers) level.
Magnifying this system to the level of the complexity of eukaryotic genomes, we
are allowed to imagine a vast system of controls acting on the same simple basis.
Lysogeny is a good example since, as the putative system controlling DNA-matrix
interaction, phage induction has only indirectly to do with transcription and gene
expression, but primarily with DNA replication, structure and organisation, and
with events of DNA rearrangement. This model may thus also provide for a quite
precise image of difference and interdependence thought to exist in between the
DNA-matrix system and the system of gene expression in the eukaryotic cell.
We are thus faced with a system whose controls will be dependent on DNA
structure and sequence, qualitative and quantitative protein (and possibly RNA)
output, and on factors modulating the capacity of the proteins to interact with
DNA, RNA and with each other. The quantitative relationship between numbers
of accepting sites in the DNA and numbers of structural and controlling proteins
available, capable of recognising and interacting selectively with such sites, is
particularly important in relation to their putative function in timing of cell
division, in quantitative and vectorial growth control discussed above. There,
morphogenesis at large is involved directly; not simply the mere capacity to
produce structural proteins "en masse", but the possibility to organise in a
sensible and crucial collaboration and cohabitation the interrelations of the
milliards of cells constituting an organism.
At this point the last problem to be discussed arises, which relates to the
possible breakdown of this system of integrative homeostasis of control. The
internal logic of the unified matrix system allows for predictions about the
consequences of disfunction of the system of DNA-matrix-RNA interaction.
Gross disfunction of the controlling factors in individual cells will lead to cell
death, of course. Such events are not only quite easily tolerated by a multicellular
organism (unless the phenomenon becomes general) but are also necessary in
some precise instances. Indeed, there is not only accidental but also programmed
cell death which is crucial in development and embryonic morphogenesis, but also
important in sexually reproducing organisms to the survival and evolution of the
species at the expense of the individual organism bound to die.
Unified Matrix Hypothesis
183
The more subtle disfunctions of the system controlling DNA-matrix-RNA
interaction will have essentially three consequences:
(1) If the matrix interactions along the D N A to R N A to protein axis, i.e. the
gene expression pathways are affected, physiological disfunction based
on altered gene expression, or on altered protodynamism, will occur.
(2) In the case of a disturbance during development of the qualitative
vectorial growth control of cellular clones, cellular or supracellular
"monsters" will develop, in which the cell to cell and organ to organ
inter-relation and, hence, the functional interactions are disorganised.
(3) Spontaneous breakdown of local growth control in a qualitative and
quantitative sense, i.e. the escape from clonal boundaries based on the
disturbance of quantitative and vectorial control of cell division, and on
loss of signal recognition from the outside, may lead to the syndrome
termed globally "cellular transformation" in both its aspects: unlimited
growth and invasiveness.
One of the attractions of the unified matrix scheme is that it seems to allow us
to relate such types of disfunction, which are well known to occur, to multiple
biochemical origins. The prediction is that lesions at DNA, R N A and protein
level may all have the same or similar effects. Furthermore, disfunction needs not
necessarily rely on a genetically fixed defect, as e.g. an altered D N A sequence
producing an aberrant protein, but may be based on altered switching at the level
of the controlling system. Faulty programming alone, independent of "hardware"
status, can thus have long term pathological effects.
It has always been and still is a mystery how such different factors as X-rays,
UV light, chemical alteration at nucleic acid or protein level, viruses, presence of
more or less of a given D N A sequence or of a given protein, all can lead to the
breakdown of organised morphogenesis, of protodynamism and growth control.
We cannot avoid observing some correlations between the mechanisms discussed
within the unified matrix scheme and some of the elements of the puzzle of
apparent contradictions and absurdity concerning cellular transformation.
It is not only the direct involvement of oncogene products in the matrix
network (Eisenmann et aL, 1985; and references therein) that calls.for attention.
Indeed, oncogene products are natural physiological cell components having
some (often unknown) function(s) in control of normal development and cell
physiology. But furthermore they seem to be localised in the cell all along the
matrix networks, from the D N A down to the plasma membrane. Some of them
are nucleic acid binding proteins, some resemble components of the structural
and membranous cell components.
Their overproduction but also their alteration and possibly inactivation, leads
to escape from physiological and developmental growth control; it is hence likely
that they participate in a system of homeostasis of control. In many aspects their
phenomenology recalls hence that of the putative DNA-matrix interactions
discussed. Oncogene products may thus correspond to some of the putative
structural components and controlling factors postulated by the unified matrix
hypothesis.
But of particular importance is the inherent conceptual possibility of viewing
cell transformation as a perfectly "normal" phenomenon. Biological agents acting
184
Scherrer
from the outside as chemicals or viruses, although responsible for most events of
transformation, are no longer conditional to explain the phenomenon of the
escape of a cell from its own homeostasis of control. And it becomes easy to
understand why a transformed cell reimplanted back into a blastula can give rise
to a normal cellular clone, as so beautifully demonstrated by Beatrice Mintz
(Mintz and Illmensee, 1975), and even in the case of the germ line (Bradley et al.,
1984).
There are a large number of correlations that could be discussed along these
lines; such an undertaking would need a second article of a size similar to this
one, and may be premature. However, we cannot avoid asking the question if in
reality cell transformation may not represent a "Matrix Disease". The future will
show if there is substance to such an allegation, which at least seems worthwhile
to be pursued theoretically and--wherever possible--by experimentation.
IN CONCLUSION
There is no point in writing a chapter of conclusions to this essay: the
conclusions were put at the beginning of our discussion, in the form of ten basic
postulates of the Unified Matrix Hypothesis. These propositions may or may not
stand up to the trial of time. It was however fascinating to undertake this
intellectual excursion since, at least apparently, it allowed the assembly of the
most unlikely pieces of a puzzle into a seemingly coherent picture.
The attempt was made here to introduce some new ideas concerning the
enigmatic molecular basis of morphogenesis and the static and dynamic organisation of the eukaryotic cell, and to propose mechanisms of its possible interdependence on still equally enigmatic characteristics of genome and DNA organisation
and function. Some ramifications of these ideas were discussed but more remain
untold. There is no space to evaluate and detail here basic knowledge on matrix
and DNA structure; the author apologizes to the eminent collegues working in
these fields for not having discussed their work which, of course, served as a basis
of reflection.
To the engaged and lucid scientist it is unacceptable to cover up our
ignorance by postulating absurdity in nature; we have the obligation to try to
push further the limits of the mechanistic comprehension of the phenomenon of
life. This idea is at the basis of this essay and is the source of its propositions as
well as of its imperfections. Sometimes we have to put to test seed and soil, being
nothing more than the humble instruments of the evolution of nature and of its
humane comprehension. And the land of Science provides time, quality and
justice to put to test such seed which will "come forth according to its kind", as so
beautifully said by Manusmriti.
ACKNOWLEDGEMENTS
The author thanks all friends and colleagues who participated by discussion
in the intellectual elaboration of this essay, and in particular the most critical and
Unified Matrix Hypothesis
185
stimulating collegues in India, who encouraged and challenged the ideas outlined
here during a lecture tour, among them in particular Pushpa Bhargava. Warm
personal thanks go to Sheldon Penman who taught me much on matrix and new
ways of looking at it, to Francois Jacob who critically evaluated the basic ideas of
the scheme, to Ron Berezney for valuable suggestions, to Franqois Zajdela,
Cecile Leuchtenberger, Jacques Moreau and Sohan Modak with whom I
discussed specific aspects, and in particular to Kinsey Maundrell who helped me
to bring ideas and language into a comprehendable from. The collaboration of
my secretary Chantal Cuisinier and of Richard Schartzmann (photography)-in
the preparation of this manuscript is gratefully acknowledged. This work was
supported by the French CNRS, INSERM, the Minist~re de la Recherche et de
la Technologie, the Fondation pour la Recherche M6dicale Franqaise and the
Association pour la Recherche sur le Cancer (ARC).
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