Epigenetic mechanism and advance in technique to study histone modification and Diseases associated with epigenetic

1. EPIGENETIC
PRESENT BY:Alireza Ahadi
A graduate student in human genetics
Beheshti University of Medical Sciences

2. Contents
Introduction
Mechanism of Epigenetics
Histone Modification
Techniques to Study Histone Modification
DNA METHYLATION
miRNAs

3. Epigenetics
DNA methylation
 - Whole Genome
Bisulphite Sequencing
Histone modification
 - Chromatin
Immunoprecipitation
Sequencing

4. Epigenetics
• Changes in gene expression or phenotype that don’t
involve changes to the DNA sequence
• Its defined as heritable changes in gene activity and expression that
occur without alteration in DNA sequence
• Modern definition is non-sequence dependent inheritance

5. Mechanism of Epigenetics
Chromatin Remodelling & Histone Modification
DNA Methylation
Non-coding RNA mediated pathway
Prion
Epigenetic code:
Consist of Both DNA methylation and histone modifications
Genetic code in each cell is the same
Epigenetic code is tissue and cell specific

6. Regulation levels

7. Epigenetics Mechanisms
Gene Expression
RNA Interference
Histone Modifications
DNA Methylation

8.  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.
 DNA wraps around histones, they also play a role
in gene regulation.
8
Luger et al., Nature 1997
Introduction
 Histones

9.  Histone proteins are of two types:
 Core Histones - H2A, H2B, H3, and H4
 Linker Histones - H1
9
 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
Types of Histones

10. 9
 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.
 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.
N-termini of the core histones
Histone Modification

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 Modifications in histone proteins affects the structure of chromatin.
 Gene regulation
 DNA damage and repair
 Chromosome condensation
Heterochromatin
-Highly packed form
- Low gene expression
Euchromatin
- Loosely packed form
- High gene
expression

12.  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,
12
Methyl Acetyl Phospho Ubiquitin SUMO
Bhaumik, Smith, and Shilatifard, 2007.
 It has been proposed that
these modifications result in a
‘code’ which can be read by
proteins involved in gene
expression and other DNA
translations
Types of Histone Modification
1. Acetylation
2. Methylation
3.Phosphorylation
4.Ubiquitination
5.Sumoylation
6. ADP ribosylation

13. Department of Plant Biotechnology 13
 The decreased HAT activity of CBP is a key contributor to
the RSTS phenotype.
 Features- Broad thumbs and toes, facial abnormalities,
congenital heart defects, and increased risk of tumor
formation.
 Frequency- This condition is uncommon; it occurs in an
estimated 1 in 100,000 to 125,000 newborns.
 Additional features of the disorder can include eye
abnormalities, heart and kidney defects, dental problems,
and obesity.
 Infants born with this severe form of the disorder usually
survive only into early childhood.
RSTS - Facial features (A), left hand and
feet showing broad thumb and big toes (B,
C) and X-ray of both hands showing short
broad thumbs (D). (Limb Malformations &
Skeletal Dysplasia)
Huda Y. Zoghbi and Arthur L. Beaudet Cold Spring Harbor
Laboratory Press, 2016
 Mutations in the CREBBP gene, the gene provides instructions for making CREB binding protein,
plays an essential role in controlling cell growth and division and prompting cells to mature
 This mutation abolishes the histone acetyltransferase (HAT) activity of CBEP (Murata et al.
2001).
03/11/2016
Diseses associated with histone modification
1. Rubinstein–Taybi Syndrome (RSTS)

14. 14
 The syndrome is caused by mutations in the RPS6KA3 gene (histone phosphorylation) and is
located on the short arm of the X chromosome. Males are usually more severely affected than
females.
 Ribosomal protein S6 kinase, 90kDa, polypeptide 3, also known as RPS6KA3, is an enzyme
that in humans is encoded by the RPS6KA3 gene.
The protein RSK2 which is encoded by the RPS6KA3 gene is a kinase which phosphorylates
some substrates like CREB and histone H3.
 A rare genetic disorder characterized by mental retardation and abnormalities of the head
and facial and other areas.
 Cardiac abnormalities affect 15% of the patients.
Coffin-Lowry syndrome
2. Coffin-Lowry syndrome
 CLSF- Coffin-Lowry Syndrome Foundation
 Created in 1991 by Mary Hoffman in France.
 CLS a general forum in which to exchange information, ideas and
advice and a great resource for families affected by CLS.

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Techniques to Study Histone Modification
i) ChIP-chip
ii) ChIP -seq
iii). ChIP-qPCR
1) Chromatin immunoprecipitation (ChIP)
i) Cross-linked ChIP (XChIP)
ii) Native ChIP (NChIP)
2) Mass Spectrometry (MS)
Other genome-wide techniques combined
with ChIPs

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1. DNA and associated proteins reversibly
cross-linked with formaldehyde followed
by cell lysis.
2. The DNA-protein complexes (chromatin-
protein) are then sheared into ~500 bp DNA
fragments by sonication or nuclease
digestion.
3. Immunoprecipitation (IP) by using an
appropriate protein-specific antibody.
4. Reverse cross linking and sequence
determination
5. Enrichment of specific DNA sequences
represents regions on the genome that the
protein of interest is associated with in vivo.
Chromatin immunoprecipitation assay (ChIP) and various methods of
analysis
Major Steps Involved in ChIP Assay

17. 17
 ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin
immunoprecipitaion ('ChIP') with DNA microarray ("chip").
 Development of genomic DNA microarrays (chips) has, when combined with ChIP assays,
enabled the mapping of transcription factor binding sites and of histone modifications.
 The most prominent representatives of this class are transcription factors, replication -related
proteins, like Origin Recognition Complex Protein (ORC), histones, their variants, and histone
modifications.
ii) ChIP–on-chip

18. 18
 Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes.
1. Crosslinking
2. Chromatin is sheared by sonication (200–600 bp )
3. Immunoprecipitation
4. Reverse crosslinking DNA is assayed to determine
the sequences bound by the protein.
5. Construction of a sequencing library,
6. Sequencing of DNA.
Overview of a ChiP–seq experiment.
ii) ChIP–seq
Major Steps
 In ChIP–seq, the DNA fragments of interest are
sequenced directly instead of being hybridized on
an array.

19. 19
 Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate
protein-DNA interaction at known genomic binding sites.
 This technique is now used in a variety of life science disciplines including cellular differentiation, tumor
suppressor gene silencing, and the effect of histone modifications on gene expression.
1. Cell fixation (cross-linking)
2. Chromatin shearing: by Sonication (100-500 bp)
3. Chromatin IP: Using specific ChIP-grade antibodies
4. Reverse cross-linking and DNA purification.
5. qPCR and analysis
Major Steps
iii) ChIP-qPCR

20. Single cell epigenetic analysis
• Epigenetic modifications directly contributed to gene
transcriptional regulation and play important roles in
tissue development and disease progression.
Considering the large heterogeneity of
transcriptional variation in cell populations, the
analysis of epigenetic modifications in single cells has
helped to better inform the detailed mechanism of
gene expression regulation.

21.  One approach is to visualize histone modifications by
combining in situ hybridization and proximity ligation
assays (PLA).
 To-date, there has been no reported success with
chromatin immunoprecipitation (ChIP) to directly
analyze histone modifications in single cells due to
the very high experimental noise to detect two
genomic DNA copies.
Single cell histone modifications

22. • However, an indirect approach called Drop-ChIP has
been reported to successfully generate the histone
modification profiles in single cells.

23. Drop-ChIP
Single cells were lysed and their chromatin
was fragmented with micrococcal nuclease
(MNase) in each drops
Drops with fragmented chromatin were
then merged with the drops carrying
different DNA barcode
DNA barcodes were ligated to the
chromatin fragments from each drop to
index them to the original cells
The merged drops were
combined and the pool of bar-coded
chromatin was then used for
immunoprecipitation by various histone
modification-specific antibodies
library preparation and sequencing

24. DNA METHYLATION
 DNA methylation is initiated by enzymes called DNA
methyl transferases (DNMTs. DNMT3a and DNMT3b.
 DNA methylation in mammalian cells typically
involves covalent addition of a methyl group (-CH3)
at the 50 position of the cytosine ring within the 50-
CpG-30 dinucleotides to create a 5-methylcytosine
(5-mC).
 CpG sites tend to cluster together as repetitive
sequences called as CpG islands (CpGI) found either
at promoters of genes.

25.  In humans, approximately 70% CpG dinucleotides are
methylated, whereas CpG dinucleotides found at
CpGI in germ-line tissues and those located near
promoters of somatic cells mostly remain
unmethylated.
• DNMT3a and DNMT3b have been shown to function
as maintenance methyl transferase in embryonic
stem cells.

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 Model for Role of Methylation in Heterochromatin Formation
 Condensation assisted by recruitment of HMT
(histone methyltransferase), where HP1
(heterochromatin protein 1) binds to H3K9-Me3
which methylates adjacent H3K9.
 Chromatin condensed until a boundary
element is reached and turned into
heterochromatin
 Methylation of histone tails long lasting
compared to acetylation.
 Can be Inherited by daughter cells:
Responsible for X-inactivation in female.

28.  the pattern of methylation of H3K4 the genome might
be formed in the embryo before de novo DNA
methylation.
 H3K4 methylation might be directed by sequence-
directed binding of RNA polymerase II, which recruits
specific H3K4 methyltransferases9.
• As RNA polymerase II is bound mostly to CpG islands in
the early embryo only these regions are marked by
H3K4me, whereas the rest of the genome is packaged
with nucleosomes containing unmethylated H3K4.

29. DIABETIC NEPHROPATHY AND DNA
METHYLATION
 Impaired insulin secretion by the pancreatic islet is a key
component to the pathogenesis of T2DM. Therefore,
several studies have used a candidate gene approach to
study the relationship between changes in DNA
methylation and gene expression in islets from donors
with T2DM.
 Increased DNA methylation was measured CpG sites
within the promoters of the pancreatic transcription
factor Pdx1, the mitochondrial gene regulator Ppargc1a
and Ins gene.

31.  Using the genomewide Infinium 450K array, 1649 CpG
sites, and 853 genes, including Tcf7l2, Fto, Kcnq1, Irs1,
Cdkn1a, and Pde7b were identified to have significant
changes in DNA methylation in human islets from T2DM
donors compared to controls.
 Increased DNA methylation at the promoter of Cdkn1a
and Pde7b was associated with decreased
transcriptional activity in clonal β-cells in vitro as well as
impaired glucose stimulated insulin secretion.

32. • Some changes in DNA methylation in peripheral tissues
have been shown to be amenable to modification by simple
physiological interventions like exercise. For example, a 6
months exercise intervention induced noticeable
alterations in genome-wide DNA methylation profile and
gene expression in adipose tissue of obese and type 2
diabetic patients.
• Epigenetics (DNA methylation) in combination with genetic
and environmental stimuli could either impair pancreatic
development and insulin secretion, or lead to insulin
resistance at peripheral tissues such as liver, muscle, and
adipose.

33. miRNAs
 MicroRNAs (miRNAs or miRs) comprise a class of short
RNA molecules, 20-23 nucleotides in length, which play a
crucial role in the regulation of gene expression at the
post-transcriptional level.
 The majority of miRNA genes are located in intergenic
regions However, they may also be found in introns of
coding and non-coding regions, as well as in exons of
certain non-protein-coding transcripts, where their
transcription is regulated together with their host exons.
 They exert their post-translational control on many basic
cellular functions, such as growth, migration and death.

35.  70% of miRNAs identified are expressed in the central
nervous system (CNS)
miRNAs and schizophrenia
 miRNAs play an important and crucial role through their
regulatory function on specific genes Specifically, miR-124
and miR-9 have been shown to play a crucial role in
neurogenesis.
 the overexpression of these miRNAs decreases the
number of astrocytes, whereas the inhibition of these
miRNAs reduces the number of neurons miRNAs.