Histone Proteins Dr. Nivedita Patnaik - PowerPoint Presentation

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 Histone Proteins

Dr. Nivedita Patnaik

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Chromatin is made of repeating units of nucleosomes, which consist of 146 base pairs of DNA wrapped around an octamer of four core

histone proteins (H3, H4, H2A and H2B)

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Introduction

Histones are a special group of proteins found in the nuclei of eukaryotic cells responsible for DNA folding and chromatin formation.

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Chemically they are-

highly alkaline basic proteins Histones are positively charged

abundance of positive amino-acids, arginine and lysine

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Classes of Histones

There are two main classes of Histones: Core Histones

Linker Histones Core Histones: In core histones following families are included H2A H2B contain more lysine H3

H4 contain more arginine

Two of each of these core histone proteins assembles to form one octameric nucleosome core particle, and 147 base pairs of DNA wrap around this core particle.

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Linker Histones

Linker histone included: H1 H5 highest lysine/arginine ratio

The linker histone protein H1 binds the nucleosome at the starting and ending sites of the DNA, thus locking the DNA into place and help in the formation of higher order structure. H5 histones are individual proteins involve in the packaging of specific region of DNA.

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Function of the histone protein in a chromosome

The DNA is housed in chromosomes in the form of nucleosomes It is basic unit of chromosome or chromatin fiber. It is DNA duplex coiled around a core of eight histone proteins

Positively charged histones are linked with negative charged phosphate groups of DNA

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Some histone proteins function as spools for the thread-like DNA to wrap around

looks like beads on a string

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The nucleosomes + H1 histones = 30 nm spiral Solenoid

It maintains the chromosomal structure

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histone modifications

Histone proteins contain a globular C-terminal domain and an N-terminal tail

The N-terminal tails of histones can undergo a variety of posttranslational covalent modifications including methylation, acetylation, ubiquitylation,

sumoylation

and phosphorylation on specific residues

regulate key cellular processes such as transcription, replication and repair

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Post-translational

histone modifications

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A

= acetylation

M

= methylation

P

= phosphorylation

U

= ubiquitination

Unlike DNA methylation, histone modifications can lead to either activation or repression depending upon which residues are modified and the type of modifications present

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Histone Acetylation & Deacetylation

Histone acetylation – Histone acetyl transferases (HATs) Adds acetyl groups to histone tails

Reduces positive charge and weakens interaction of histones with DNA Facilitates transcription by making DNA more accessible to RNA polymerase II Histone deacetylation – Histone deacetylases (HDACs) Removes acetyl groups from histone tails

Increases interaction of DNA and histones

Represses transcription

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Acetylation

It is the introduction of an Acetyl functional group to the Lysine amino acid of the histone tail. These reactions are

catalyzed by enzymes with "histone acetyltransferase" (HAT) or "histone deacetylase" (HDAC) activity.

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Effects of Acetylation

-ve charge on histone. reduces affinity of tail for adjacent nucleosomes

creating a transcription permissive environment increase the access of transcription factors

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Methylation

It is the introduction of an Methyl functional group to Lysine or Arginine of the histone tail.

These reactions are catalysed by enzymes with "histone methyltransferase” ‘Arg’ can be methylated once or twice, and ‘Lys’ once, twice or thrice.

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Histone Methylation

Histone methyl transferases (HMTs) Histone lysine methyl transferases(HKMTs) methylate

lys (K) residues Protein argenin methyl transferase (PRMTs) Methylate arge

(R) residues

Methylation can result in activation or repression of expression

trimethylation of histone H3 at lysine 4 (H3K4) is an active mark for transcription

dimethylation

of histone H3 at lysine 9 (H3K9), a signal for transcriptional silencing

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Effects of methylation

Methylation does not neutralize charge but recruit silencing or regulatory proteins that bind methylated histones. Chromodomain containing proteins interact with methylated histone tails.

transcription repression

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Histone phosphorylation (H3)

Histones are phosphorylated during mitosis.Histones are also phosphorylated by signal transduction pathways like the ERK pathway in response to external signals. It is not known how (and if) this phosphorylation contributes to gene expression.

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Histone ubiquitylation

Addition and removal of Ub (a LARGE moiety) to histone tails –

Functions largely unknown in vertebratesubiquitylationH2A K119: repressionH2B K120: activation

H3 and H4: DNA repair (CUL4)

de-ubiquitylation –

Recrutiment

of other proteins in yeast

H2A Dub (PCAF)

H2B Ubp8 (SAGA)

Functions

: transcription

elongation

,

polycomb

repression

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Study of histone modifications

Histone modifications are studied using the chromatin immunoprecipitation (ChIP) assay.

ChIP on chip is the high throughput form of the ChIP assay wherein the immunoprecipitated DNA, instead of being subject to the usual PCR, is hybridized to a microarray chip with printed oligonucleotides corresponding to various regions of the genome.

This helps to study the localization of a specific histone modification to various parts of the genome.

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Epigenetic therapy

DNMT INHIBITORS

1.Nucleoside analogue inhibitors

2.Non nucleoside analogue inhibitors

3.Antisense oligonucleotides

HDAC INHIBITORS

1.Hydroxamates

2.Cyclic tetrapeptides

3.Aliphatic acids

4.Benzamides

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DNMTi

Nucleoside analogs

5 aza cytidine,

5 aza 2' deoxy cytidine (

decitabine)

Leads to DNA demethylation

Reactivate epigenetically silenced genes

Used in MDS.

Zebularine, oral, less toxic, under trial

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Epigenetic therapy

HDACi

SAHA (

Vorinostat

)

,

Depsipeptide

Leads to

hyperacetylation

Activation of silenced pro-apoptotic genes

Pro-apoptotic genes are

upregulated

Lead to apoptosis in cancer cells.

Cutaneous

T cell lymphoma

EZH2i

Deazaneplanocin

Activate apoptotic cell death in breast cancer

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Primary

nonsmall cell lung cancer (NSCLC) is the main cause of malignancy-related mortality in Asian and Western populations.positive correlation between lower levels of H3K9ac, H3K9me3 and H4K16ac and

tumor recurrence. However when patients were further clustered according to histone modification patterns (i.e.

acetylation

dominant,

methylation dominant, co-dominant and modification negative), the acetylation-dominant group exhibited

better survival prognosis, but methylation dominant and

modification negative status was associated with poor prognosis

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THANK YOU