Nucleosome, Histone proteins, Histone modifications

1. B Y : D R . S O N I A G O E L
S G T U N I V E R S I T Y , G U R U G R A M
HISTONE MODIFICATIONS

2. HISTONE
 Histones are a group of basic protein that associate with
DNA and help the DNA to condense it into chromatin.
 Histones contain a large proportion of the positively charged
(basic) amino acids, lyseine and arginine in their structure.
 DNA is negatively charged due to the phosphate groups on its
backbone.
 These result of these opposite charges is strong attraction and
therefore high binding affinity between histones and DNA
structure called nucleosome.

3.  DNA wraps around histones, they also play a role in gene
regulation.
 The basic unit of chromatin is the nucleosome core particle, 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.

5. Types of Histones
 Core Histones - H2A, H2B, H3, and H4
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. HISTONE MODIFICATION
 N-terminal tails of histones are the most accessible regions of these
peptide as they protrude from the nucleosome and possess no specific
structure.
 The major function of PTMs is to either create sites for the
recruitment of specific factors or modify existing sites so as
to abolish previous interactions.
 Chromatin must be first made relaxed to allow access of cellular
machineries to chromatin DNA.

8.  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 modification (PTM) of histones is a crucial step in
epigenetic regulation of a gene.

9.  Modifications in histone proteins affects the structure of chromatin.
 Gene regulation
 DNA damage and repair
 Chromosome condensation

10. 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,
 Acetylation
 Methylation
 Phosphorylation
 Ubiquitination
 Sumoylation
 ADP ribosylation

11. Some Examples of Histone Modification and Modifiers

12. Acetylation
 N-term tails reversible acetylated in Lys, particularly in H3+H4
 While the globular core is involved in histone-histone packing and
 DNA-contact, the N-terminal tails point outwards and is available for
interaction.
 Acetylation also provides binding sites for a number of proteins with an
approximately 100-amino-acid sequence motif called a bromodomain.

16. Methylation
 It is the introduction of an Methyl functional group to only on Lysine
or Arginine of the histone tail.
 These reactions are catalyzed by enzymes with "histone
methyltransferases (HMTs)”
 Histone lysine methyl transferases (HKMTs) Methylate lysine (K)
residues
 Protein argenin methyl transferases (PRMTs) Methylate arginine (R)
residues
 A role in both activation and repression . Arginines can be
mono- or dimethylated whereas lysines can be mono-, di- or
trimethylated

17.  Methylation can result in activation or repression of expression .
 Activation (H3K4, H3K36, H3K79)
 Trimethylation of histone H3 at lysine 4 (H3K4) is an universal active
mark for transcription.
 Repression (H3K9, H3K27, H4K20)
 Dimethylation of histone H3 at lysine 9 (H3K9) and at 27 (H3K27)
are the universal signal for transcriptional silencing.

19. Phosphorylation
 Phosphorylation is the addition of a phosphate group (PO4 3−) to a
molecule.
 Phosphorylation is catalyzed by various specific protein kinases,
whereas phosphatases mediate removal of the phosphate group.
 Histones can also get phosphorylated and the most studied sites of
histone phosphorylation are the serine 10 of histone H3 (H3S10) that
is deposited by the Aurora-B kinase during mitosis.

21. 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 main steps: activation, conjugation, and
ligation, performed by ubiquitin-activating enzymes (E1s), ubiquitin-
conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively.

23. Sumoylation
 Small Ubiquitin-like Modifier (or 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 was first reported in 2003, when Shiio et al. found that H4 can
be modified by SUMO and they suggested that this modification leads to the
repression of transcriptional activity through the recruitment of HDACs
and HP1 proteins
 The putative sumoylation sites were identified as K6/7 and to a lesser
extent K16/17 of H2B, K126 of H2A, and all four lysines in the N-
terminal tail of H4.
 Histone sumoylation has a role in transcription repression by opposing other
active marks such as acetylation, methylation, ubiquitination etc.

25. ADP-Ribosylation
 ADP-ribosylation is the addition of an ADP-ribose moiety onto a
protein using NAD+ as a substrate.
 Mono(ADP-ribosyl)ation is mediated by ADP ribosyl transferases
(ART) and the enzymes responsible for the PARation (Poly-ADP-
ribosylation) are the poly(ADPribose) polymerases (PARPs).
 PARP1 prefers to linker histone H1 while PARP2 prefers core histones.
 H1 to nucleosomes increases chromatin compaction, ADP-ribosylation
of H1 is suggested to alter the chromatin structure and possibly the
chromatin composition.

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