Transcription and chromatin
General Transcription Factors +
Promoter-specific factors +
Co-activators
Cofactor or Coactivator
1. work with DNA specific transcription factors to
make them more effective - examples
A. TFIID
B. yeast mediator - contains 20 polypeptides
binds to the CTD of RNA polymerase II
C. CBP/p300 works with CREB protein
D. TRAPS - steroid receptor protein cofactor
E. OCA-B with Oct 1 protein
F. SAGA complex - contains Ada proteins
(adaptor protein) one of which is also known as
Gcn5; works with acidic activators such as Gal4
protein or Gal4-VP16
Cofactor or Coactivator
2. Several of these proteins modify
chromatin; acetylation of histone tails
A. TAFII 250
B. Gcn5 is one of the first
characterized histone acetyl transferases
(HAT)
C. CBP/p300
Gaining Access to the DNA
Large multi-subunit protein
complexes alter the state of
chromatin
Organization of Chromatin
Proposed 30nm fiber structure
Schalch, T et. al., Nature. 2005;436:138-41.
Gary Felsenfeld & Mark Groudine, Nature, 2003; 421:448-53.
What is chromatin remodeling?
The process of making DNA more or less
accessible in the eukaryotic genome using
a series of specialized proteins
Chromatin Remodeling
• ATP-dependent chromatin remodeling
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SWI/SNF and RSC
ISWI: CHRAC, NURF, ACF
CHD/Mi-2
INO80 and SWR1
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ACETYLATION
METHYLATION
PHOSPHORYLATION
UBIQUITINATION
Poly ADP RIBOSYLATION
SUMOLYATION
• Covalent modification
What is the functional role of
chromatin remodeling
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Global regulation of chromatin structure
Transcription activation and repression
Transcription elongation and termination
DNA repair
DNA recombination
– including immunoglobulin gene rearrangement
• DNA replication
ATP-dependent chromatin
remodeling machines
A. they alter the structure of the nucleosome
i. the nucleosomal DNA is made more
accessible for binding to transcription factors
ii. changes can also be observed by measuring
access to cutting by restriction endonucleases
iii. changes have also been observed in DNA
supercoiling suggesting a change in the path of
DNA around the nucleosome
iv. electron microscopy studies have suggested
a reduction on the amount of DNA wrapped in the
remodeled nucleosome
ATP-dependent chromatin
remodeling machines
b. Slides nucleosomes along DNA, changes their
translational position
i. changes in electrophoretic mobility is observed
ii. micrococcal nuclease mapping also shows
changes in translational positioning
c. Spaces and assembles nucleosomes
Sliding Nucleosomes
Spacing nucleosomes
Nucleosomes are randomly distributed along DNA
Located equal distances from each other
(uniformly spaced, but no uniquely positioned)
These complexes can be recruited to
specific chromatin sites by:
A. transcriptional activators such as
SWI/SNF by Gal4, Gcn5 and the
glucocorticoid receptor protein
B. repressors such as the ISWI complex
from yeast called ISW2 by the Ume6
repressor protein
Accessibility is Key Regulatory Step
ATP-dependent chromatin
remodeling machines
Different classes of chromatin
remodeling complexes
Different classes of ATP-dependent
chromatin remodeling complexes
A. SWI/SNF or SWI-SNF like complexes
– required for activation of a small subset of
genes
– found in humans, flies, and yeast
– at least two different forms of the complex in
yeast or humans
– in yeast it has 11 or 17 subunits
– total complex size is 1.5 -2 Megadaltons
Mammalian SWI/SNF
Wiley-Liss, Inc.
Different classes of ATP-dependent
chromatin remodeling complexes
B. ISWI or imitation SWI complexes
-its DNA dependent ATPase subunit is
similar to the ATPase subunit of SWI/SNF
-has the distinguishing protein domain called
SANT
-smaller complexes: only 1-4 subunits
-more abundant and play a more global role
-are involved in transcriptional repression
- there are three distinct ISWI complexes in
flies and yeast
ISWI Subfamily of Chromatin Remodeling
Complexes
Corona, D.F. and J.W. Tamkun, Multiple roles for ISWI in transcription, chromosome organization and DNA replication.
Biochim Biophys Acta, 2004. 1677(1-3): p. 113-9.
Remodeling Activities of ISWI Subfamily
Langst, G. and P.B. Becker, Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors.
J Cell Sci, 2001. 114: p. 2561-8.
Different classes of ATP-dependent
chromatin remodeling complexes
C. Mi-2 or CHD complexes
-these chromatin remodeling complexes are
associated with histone deacetylases (HDAC)
- ATPase subunit has sequence homology to
the ATPase subunit of SWI/SNF belongs to the
Swi2 superfamily, but makes up its own
subfamily
Different classes of ATP-dependent
chromatin remodeling complexes
D. INO80 complex
-involved in DNA repair
-has DNA helicase activity associated
with the complex
E. SWR1 complex
-promotes the exchange of H2A from
the nucleosome
-brings in a H2A variant called H2AZ
Chromatin Remodeling Complexes Are
Classified by the ATPase Subunits
SNF2
ISWI
Mi-2
INO80
Helicase
Bromo
AT Hook
HAND
SLIDE
Chromo
PHD
DBINO
SANT
Mechanisms of ATP-dependent
chromatin remodeling
Several models involving DNA
bulges or DNA twist
Twist diffusion model
Would move nucleosomes in 1 bp increments
Flaus and Owen-Hughes Biopolymers 2003
Least disruptive of histone-DNA contacts
Bulge Propagation Model
Planar bulge
Propagation of bulge in a
wave-like manner
around the nucleosome
Flaus and Owen-Hughes Biopolymers 2003
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