1. Chromatin remodeling complexes use ATP hydrolysis to modify nucleosome structure and expose DNA for gene expression. The main classes are ATP-independent complexes and ATP-dependent complexes like ISWI and SWI/SNF. 2. Post-translational modifications of histone tails like acetylation, methylation, and phosphorylation can affect chromatin structure and transcription by altering DNA-histone interactions. 3. Chromatin remodeling is important for differential gene expression in specialized cell types and controlling DNA accessibility for transcription.

1. K. Narayanapura, Kothanur (PO), Bengaluru 560077
www.kristujayanti.edu.in
Chromatin Remodelling
Dr. Manikandan Kathirvel
Assistant Professor,
Department of Life Sciences,
Kristu Jayanti College (Autonomous),
Bengaluru

2. Chromatin Remodeling
• Chromatin structure provides an important level of control of gene
transcription.
• The development of specialized organs, tissues, and cells and their function in
the intact organism depend upon the differential expression of genes.
• Some of this differential expression is achieved by having different regions of
chromatin available for transcription in cells from various tissues.
Large regions of chromatin are
transcriptionally inactive in some cells,
while they are either active or
potentially active in other specialized
cells.
For example, the DNA containing the -
globin gene cluster is in "active"
chromatin in the reticulocytes but in
"inactive" chromatini n muscle cells.

3. MAJOR CLASSES OF CHROMATIN-REMODELING
COMPLEXES
Chromatin
remodeling
complex
ATP Independent
modeling complexes
ATP Dependent
modeling complexes
Histone modifications
The ATP dependent remodeling
complexes require ATP hydrolysis for
modification of architecture of
nucleosome which helps to expose
the required sequence in DNA for
gene expression.
The enzymes are as follows:
ISWI (imitation switch )
SWI/SNF (Switching of mating
types/ sucrose non fermenting)

4. EFFECTS OF HISTONES ON TRANSCRIPTION ACTIVATION
 Histone modification – post
translational modification includes
methylation, phosphorylation,
acetylation, ubiquitylation,
summoylation.
 DNA wrap around the histone
octamer in a structure like beads
on string ,which makes the basic
chromatin unit.
 Chromatin folds into higher level
structures, helps to determine the
DNA accessibility.
 The transcriptional machinery
cannot access the DNA and genes
remain inactive.

5. Histones
 Histones are a group of basic proteins that
associate with DNA to condense it into
chromatin.
 Histones contain a large proportion of the
positively charged (basic) amino acids ,
lysine and arginine in their structure.
 DNA is negatively charged due to the
phosphate groups on its backbone.
 The results of these attraction and therefore
high binding affinity between histones and
DNA structure called nucleosomes.
 DNA wraps around histones, they also
play a role in gene regulation.
 The basic unit of chromatin is the
nucleosome core particles, which contains
147 bp of DNA wrapped nearly twice around
an octamer of the core histones.
 Each nucleosome is separated by 10-60 bp
of “linker” DNA, and the resulting
nucleosomal array constitutes a chromatin
fiber of 10 nm in diameter.

6.  Two types of Histones:
1) Core Histones- H2A, H2B, H3,
H4
2) Linker Histones- H1
 The eight histones in the core are
arranged into a (H3)2(H4)2
tetramer and a pair of H2A-H2B
dimers.
 The tetramer and dimers come
together to form a left- handed
superhelical ramp around which
the DNA wraps.
 Hydrogen bonds between the
DNA backbone and the amide
group on the main chain of
histone proteins.

7. Formation and disruption of
nucleosome structure:
• The presence of nucleosomes
and of complexes of histones and
DNA provide a barrier against the
ready association of transcription
factors with specific DNA regions.
1. Chromatin composed of cells DNA and
associated proteins.
2. There are five histone proteins in the family
H1,H2A,H2B,H3,and H4.
3. Two H3 and two H4 proteins form a tetramer
which combines with two H2A,H2B dimers to
form the disk shaped histone core .
4. 150bp of DNA wrap around the protein about
twice making a nucleosome core particle with
linker histone and linker DNA.
5. Linker DNA varies in length ( 10 and 90bp).
6. Nucleosome repeats every 200bp and is close to
10nm diameter.

8. Histone modification
 N-terminal tails of histones are the most
accessible regions of these peptides as they
protrude from the nucleosome and possess
no specific structure.
The amino-terminal portion of the core histone proteins contains a flexible and
highly basic tail region, which is conserved across various species and is
subject to various PTM.
Chromatin can be highly packed or loosely packed, and correlated to the gene
expression levels.
Post-translational modifications(PTM) of histones is a crucial step in
epigenetic regulation of a gene.
Modifications in histone proteins affects the structure of chromatin.
Gene regulation
DNA damage and repair
Chromosome condensation

9. Types of histone modification
 N-terminal tails of all histones are particularly of interest since they
protrude out of the compact structure. These N-terminal tails are often
subjected to a variety of post-translational modifications such as,
a) Acetylation
b) Methylation
c) Phosphorylation
d) Ubiquitination
e) Sumoylation
f) ADP ribosylation

10. The disruption of nucleosome structure
is therefore an important part of
eukaryotic gene regulation and the
processes involved are as follows:
i) Histone acetylation and deacetylation
Acetylation is known to occur on lysine
residues in the amino terminal tails of
histone molecules.
This modification reduces the positive
charge of these tails and decreases the
binding affinity of histone for the
negatively charged DNA.
Accordingly, the acetylation of histones
could result in disruption of
nucleosomal structure and allow
readier access of transcription factors
to cognate regulatory DNA elements.

11. N-terminal tails are
reversible
acetylated in Lys,
particularly in
H3+H4.
 Acetyl group
addition to
lysine in histone
tails loosens
nucleosome
grip on DNA by
neutralizing
positive charge.
i) Histone acetylation and deacetylation

12. i) Histone acetylation and deacetylation

13. ATP INDEPENDENT REMODELING COMPLEX

14. ii) Methylation
 It is the introduction of an methyl functional group to only on Lysine or Arginine
of the histone tail.
 These reactions are catalysed by enzymes like histone methyltransferases
(HMTs).
 Histone lysine methyl transferases (HKMTs) methylate Lysine (K) residues.
 Protein argenine methyl transferases (PRMTs) methylate Arginine (R)
residues.
 A role in both activation and repression.
 Arginines can be mono or di methylated whereas lysines can be mono, di , tri
methylated.

15. ii) Methylation
Methylation of deoxycytidine residues in DNA may effect gross changes
in chromatin so as to preclude its active transcription.
Example: Acute demethylation of deoxycytidine residues in a specific region of
the tyrosine aminotransferase gene—in response to glucocorticoid hormones—has
been associated with an increased rate of transcription of the gene.

17. iii) Ubiquitination
 Ubiquitination (or ubiquitylation)
refers to the post translational
modification of the amino group of a
lysine residue by the covalent
attachment of one
(monoubiquitination) or more
(polyubiquitination) ubiquitin
monomers.
 Ubiquitin is a 76 amino acid protein
highly conserved in eukaryotes.
 Histone Ubiquitination alters
chromatin structure and allows the
access of enzymes involved in
transcription.
 Ubiquitination is carried out in three
steps: activation, conjugation and
ligation, performed by ubiquitin-
activating enzymes (E1s), ubiquitin-
conjugating enzymes (E2s) and
ubiquitin ligases (E3s), respectively.

18. v) Sumoylation:
 Small ubiquitin like modifier
(SUMO) proteins are a
family of small proteins that
are attached to and
detached from other
proteins in cell to modify
their function.
 Sumoylation consists in the
addition of a small ubiquitin
related modifier protein
(SUMO) of 100 amino acids.
 Histone Sumoylation has a
role in transcription
repression by opposing
other active marks such as
Acetylation, methylation,
Ubiquitination, etc.
iv) Phosphorylation
 Phosphorylation is the addition of a
phosphate group (PO43-) to a
molecule.
 Phosphorylation is catalyzed by
various specific protein kinases.
 Histones are phosphorylated and the
most studied sites of histone
Phosphorylation are the serine 10 of
histone H3 (H3S10)

19. vi) DNA binding proteins
•The binding of specific transcription factors to certain DNA elements may result
in disruption of nucleosomal structure.
•Many eukaryotic genes have multiple protein-binding DNA elements.
•The serial binding of transcription factors to these elements may either directly
disrupt the structure of the nucleosome or prevent its re-formation.
•These reactions result in chromatin-level structural changes that in the
end increase DNA accessibility to other factors and the transcription
machinery.

20. Studies postulate that SWI2/SNF2 and related proteins can function
to destabilize nucleosome structure and thereby to facilitate the
binding of transcription factors to chromatin.
SWI2/SNF2:
Genetic studies of transcriptional regulation in Saccharomyces cerevisiae led to
the identification of a number of SWI and SNF genes (SWI refers to yeast
mating type swi tching, while SNF is an abbreviation for s ucrose n on f
ermenting.
The gene encoding the first SNF2/SWI2 enzyme was discovered by the yeast
geneticists Ira Herskowitz and Marian Carlson in the 1980s.

21. SNF2 protein
A SNF2 protein is an enzyme that belongs to the SF2 helicase-
like superfamily, and it is the founding member of a subfamily of
enzymes called SNF2-like helicases, which all harbor a conserved
helicase-related motifs similar to SNF2.
The SNF2 family proteins have multiple members, which are
approximately 30 different enzymes in human cells and 17
different enzymes in budding yeast.
SNF2 enzymes can be further classified into six groups
based on the structure of the helicase domain. These groups
are Swi2/Snf2-like, Swr1-like, SS01653-like, Rad54-like, Rad5/6-
like, and distant (SMARCAL1) enzymes.
 Many of the SNF2 enzymes have been shown to remodel
chromatin in vitro in an ATP-dependent manner, and several
enzymes remain to be tested.

22. SWI2/SNF2 Complex:
Experiments revealed that the SWI/SNF complex possesses a DNA-
stimulated ATPase activity and can destabilize histone-DNA
interactions in reconstituted nucleosomes in an ATP-dependent
manner, though the exact nature of this structural change is not known.
In addition, this SWI2/SNF2-mediated destabilization of nucleosomes was
found to increase the binding of transcription factors, such as GAL4
derivatives or the TATA box-binding protein (TBP), to the histone-associated
DNA.
These results, combined with the genetic data, led to the hypothesis that the
SWI/SNF complex facilitates the binding of transcription factors to
chromatin.

24. A Simple Model Depicting a Suggested
Mechanism for the Destabilization of
Nucleosomes by SWI/SNF Complex
and Related Factors by ATP-Driven
Translocation of the Protein along
Nucleosomal DNA
ATP DEPENDENT REMODELING
COMPLEXES

25. Members of the SNF2-like family exhibit an impressive range of
biological functions.
These activities include
•gene-specific transcriptional activation,
•transcriptional repression,
•destabilization of reconstituted nucleosomes,
•transcription-coupled repair,
•nucleotide excision repair of nontranscribed regions of the
genome,
•recombination repair,
•and chromosome segregation.
SNF2-like family members are also involved in human disease.
•Mutations in the human ERCC6 gene can lead to Cockayne's syndrome,
which is characterized by progressive neurodegeneration, dwarfism,
photosensitivity, and developmental abnormalities.
• In addition, mutated forms of the human ATR-X gene (also known
as NUCPRO; tentatively assigned to the RAD54 subfamily) cause a
combined α-thalassemia and mental retardation syndrome

26. NURF—A Complex Containing ISWI, a
Member of the SNF2L Subfamily
The analysis of an ATP-dependent activity
that is required to alter nucleosome
structure upon binding of the GAGA
transcription factor (a sequence-specific
DNA-binding factor in Drosophila) has led
to the purification of a factor termed NURF
(Nucleosome Remodeling Factor) from
Drosophila embryos.
NURF is an ∼0.5 MDa complex that
contains four polypeptides, one of which is
the ISWI (imitation switch) protein.
ISWI is a member of the SNF2L subfamily,
which is closely related to the SNF2
subfamily. At present, downstream targets
of ISWI are not known.
ISWI, a Member of the SWI2/SNF2
ATPase Family, Encodes the 140 kDa
Subunit of the Nucleosome Remodeling
Factor