Plant Cell Advance Publication. Published on February 11, 2016, doi:10.1105/tpc.16.00113
IN BRIEF
The Plant Cell Reviews Small RNA Dynamics: From Small Genetic Circuits to Complex Genomes
Small RNAs play a large role in many biological
processes, from the regulation of protein
coding genes during growth and development
to the control of transposable element (TE)
activity and genome dynamics on an
evolutionary timescale. This issue of The Plant
Cell includes four new review articles that
explore aspects of small RNA function,
transcriptional control, TE silencing, and
epigenetic patterns that shape plant genomes.
Fang and Qi (2016) highlight recent
progress towards our understanding of the
mechanisms and functions of plant Argonaute
(AGO) proteins. Small RNAs of all types
associate with AGO proteins to form RNAinduced silencing complexes (RISCs) to
silence target genes or TEs via several
different modes of action (Figure 1). Plant
AGOs have expanded during evolution and fall
into three major clades (AGO1/5/10,
AGO2/3/7, and AGO4/6/8/9) that show
functional differences. Fang and Qi review the
general features and phylogeny of plant AGOs
and mechanisms of RISC assembly and
modes of action of AGO complexes, and
discuss recent progress in understanding the
roles of AGOs in plants. Remaining challenges
include identifying AGO cofactors and
investigating the potential for AGO functions
independent of the canonical RNAi pathways.
Megraw et al. (2016) review small genetic
circuits that regulate transcription mediated by
RNA Polymerase II (pol-II), focusing in
particular on small RNA regulatory circuits
containing pol-II transcribed microRNAs
(miRNAs). The authors suggest that the
relative simplicity of tissue and cellular
organization, miRNA targeting and genomic
structure in plants, particularly Arabidopsis,
make this model uniquely amenable for small
RNA regulatory circuit studies. The article
provides an introduction to analysis and
validation methods for investigating miRNAcontaining regulatory circuits, such as the
Figure 1. Modes of Action of Plant AGO Proteins. (A) AGO1 binds miRNAs or ta-siRNAs and
cleaves target mRNAs. (B) AGO1 binds miRNAs and inhibits the translation of target mRNAs.
(C) Arabidopsis AGO10 and rice AGO18 act as decoys for miR165/166 and miR168, respectively.
(D) AGO4 binds hc-siRNAs or lmiRNAs and mediates DNA methylation. (E) AGO2 binds diRNAs and
mediates DSB repair. [Reproduced from Fang and Qi (2016), Figure 2.]
identification of pol-II start sites and
transcription factor binding sites. The authors
explore the important roles of these circuits in
plant function and summarize opportunities for
new plant studies, making the important
observation that new genome editing
techniques (e.g. CRISPR-Cas) will only
become truly powerful when the outcome can
be predicted.
Sigman and Slotkin (2016) review TE
silencing
mechanisms
in
different
chromosomal contexts: near a gene, within a
gene, in a pericentromere / TE island, or at the
centromere core, and posit that chromosomal
location is the first rule dictating the regulation
of TEs. Dynamic regulation works to maintain
tight boundaries of methylation between a TE
and neighboring genes or a TE located within
an actively transcribed gene. A neighboring TE
can influence gene activity, which occasionally
may produce a stable epiallele, as in the case
of maternally imprinted genes and some genes
involved in pathogen and pest resistance. Most
TEs within genes are inactive, likely due to
strong selection against this form of
mutagenesis, and plants have evolved
mechanisms maintaining strict coordination
between TE silencing and gene activity.
Pericentromeres, knobs, and TE islands
typically have a large number of TEs, which are
silenced by the chromatin-remodeling protein
DDM1, and the size of TE islands is correlated
with overall plant genome size. TEs affect
chromosome core structure and a key future
research question is whether TE regulation in
this region has a role in specifying centromere
function.
Springer et al. (2016) explore the notion
that chromatin structure and silencing
mechanisms of plant genomes have been
shaped by TE bursts and whole genome
duplication (WGDs), resulting in variation in
epigenomic patterns among different species
(Figure 2). They suggest that the chromatin
modifications and epigenetic regulation
associated with TEs may play a role in
©2016 American Society of Plant Biologists. All Rights Reserved.
mediating the effects of WGD events,
especially during allopolyploid events that
combine genomes with distinct TEs. The
interactions
of
heterochromatin
and
euchromatin have important roles in
modulating gene expression and variability
within species. These are especially important
features of the complex genomes of many crop
species, which have evolved chromatin-based
mechanisms to tolerate silenced TEs near
actively expressed genes. Increasing our
understanding of chromatin diversity and
regulation can improve our ability to select or
engineer ideal crop varieties and to stabilize
performance in these lines.
These reviews underscore the value and
utility of basic plant research: an important
underlying theme in all of these articles is that
chromatin state plays a large role in many
biological processes and yet is relatively
understudied and many fundamental
questions remain unanswered. We have
Figure 2. Striking differences in genome and epigenome organization in different
plant species. The organization of genes (green) and TEs (pink) is shown for portions of
the maize and Arabidopsis genome, along with the relative abundance of chromatin
modifications often associated with heterochromatin: CHG DNA methylation (red), CHH
DNA methylation (black) and H3K9me2 methylation (blue). [Reproduced from Springer et
al. (2016), Figure 1].
powerful genome-editing tools at our fingertips,
but do not yet fully understand the functions of
AGO proteins in gene regulation, especially in
crop species (Fang and Qi, 2016) or what
constitutes a "core promoter" in the majority of
plant genes (Megraw et al., 2016) or how TE
regulation and chromatin state may affect
centromere function (Sigman and Slotkin,
2016) or crop performance (Springer et al.,
2016). These articles provide timely updates
on aspects of small RNA-mediated processes
in plants, and help to point the way forward
toward furthering our understanding of plant
function and evolution.
Nancy A. Eckardt
Senior Features Editor
[email protected]
ORCID ID: 0000-0003-1658-1412
REFERENCES
Fang, X., and Qi, Y. (2016). RNAi in Plants: An
Argonaute-Centered View. Plant Cell
10.1105/tpc.15.00920.
Megraw, M., Cumbie, J.S., Ivanchenko,
M.G., and Filichkin, S.A. (2016). Small
Genetic Circuits and microRNAs: Big Players
in Pol-II Transcriptional Control in Plants.
Plant Cell 10.1105/tpc.15.00852.
Sigman, M.J., and Slotkin, R.K. (2016). The
First Rule of Plant Transposable Element
Silencing: Location, Location, Location.
Plant Cell 10.1105/tpc.15.00869.
Springer, N.M., Lisch, D., and Li, Q. (2016).
Creating order from chaos: epigenome
dynamics in plants with complex genomes.
Plant Cell 10.1105/tpc.15.00911.
The Plant Cell Reviews Small RNA and Chromatin Dynamics: From Small Genetic Circuits to
Complex Genomes
Nancy Eckardt
Plant Cell; originally published online February 11, 2016;
DOI 10.1105/tpc.16.00113
This information is current as of July 31, 2017
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