chromatin structure & dynamics
DESCRIPTION
Chromatin Structure & Dynamics. Victor Jin Department of Biomedical Informatics The Ohio State University. Chromatin. Walther Flemming first used the term Chromatin in 1882. At that time, Flemming assumed that within the nucleus there was some kind of a nuclear-scaffold . - PowerPoint PPT PresentationTRANSCRIPT
Chromatin Structure Chromatin Structure & Dynamics& Dynamics
Victor JinDepartment of Biomedical InformaticsThe Ohio State University
Chromatin Walther Flemming first used the term Chromatin in 1882. At that
time, Flemming assumed that within the nucleus there was some kind of a nuclear-scaffold.
Chromatin is the complex of DNA and protein that makes up chromosomes.
Chromatin structure: DNA wrapping around nucleosomes – a
“beads on a string” structure.
In non-dividing cells there are two types of chromatin: euchromatin and heterochromatin.
Chromatin Fibers
30 nmchromatin fiber
11 nm(beads)
Chromatin as seen in the electron microscope. (source: Alberts et al., Molecular Biology of The Cell, 3rd Edition)
The basic repeating unit of chromatin.
It is made up by five histone proteins: H2A, H2B, H3, H4 as core histones and H1 as a linker.
It provides the lowest level of compaction of double-strand DNA into the cell nucleus.
It often associates with transcription.
Nucleosome
H2A H2BH3
H4
1974: Roger Kornberg discovers nucleosome who won Nobel Prize in 2006.
Core Histones are highly conserved proteins - share a structural motif called a histone fold including three α helices connected by two loops and an N-terminal tail
Histone Octamer
Each core histone forms pairs as a dimer contains 3 regions of interaction with dsDNA; H3 and H4 further assemble tetramers. The histone octamer organizes 146 bp of DNA in 1.65 helical turn of DNA: 48 nm of DNA packaged in a disc of 6 x 11nm
< 6 nm >
<
11
nm
>
Nucleosome Assembly In Vitro
4 core histones + 1 naked DNA template at 4C at 2M salt concentration, from Dyer et al, Methods in Enzymology (2004), 375:23-44.
DNA compaction compaction in a human cell nucleus
1bp (0.3nm)
10,000 nm
30nm
11 nm
The N-terminal tails protrude from the core
Histone Modifications
Me
P
Ub
Su
Ac Me
Acetylation
Methylation
Ubiquitination
Sumoylation
Phosphorylation
‘Histone Code’
Acetylation of LysinesAcetylation of the lysines at the N terminus of histones removes positive charges, thereby reducing the affinity between histones and DNA.
This makes RNA polymerase and transcription factors easier to access the promoter region.
Histone acetylation enhances transcription while histone deacetylation represses transcription.
Methylation of Arginines and Lysines
Arginine can be methylated to form mono-methyl, symmetrical di-methyl and asymmetrical di-methylarginine.
Lysine can be methylated to form mono-methyl,
di-methyl and tri-methylarginine.
Methylation of Histone H3-K27
K27
PCDNMT
SUZ12HDACEED
EZH2
Functional Consequences of Histone Modification
Establishing global chromatin environment, such as Euchromatin, Heterochromatin and Bivalent domains in embryonic stem cells (ESCs).
Orchestration of DNA-based process transcription.
Euchromatin
A lightly packed form of chromatin; Gene-rich; At chromosome arms; Associated with active transcription.
Heterochromatin
A tightly packed form of chromatin; At centromeres and telomeres; Contains repetitious sequences; Gene-poor; Associated with repressed transcription.
Bivalent Domains
Poised state. The chromatin of embryonic stem cells has “bivalent” domains with marks of both gene activation and repression. In these domains, the tail of histone protein H3 has a methyl group attached to lysine 4 (K4) that is activating and a methyl group at lysine 27 (K27) that is repressive (above). This contradictory state may keep the genes silenced but poised to activate if needed. When the cell differentiates (right), only one tag or the other remains, depending on whether the gene is expressed or not.
DNA Methylation
5-methylcytosine
S-adenosylmethionine
DNA methyltransferase
deoxycytosine
N
N
O
OH H
-OO
N
N
N
O
OH H
-OO
NCH3
CpG Islands
CpG island: a cluster of CpG residues often found near gene promoters (at least 200 bp and with a GC percentage that is greater than 50% and with an observed/expected CpG ratio that is greater than 0.6).
~29,000 CpG islands in human genome (~60% of all genes are associated with CpG islands)
Most CpG islands are unmethylated in normal cells.
Mark Transcriptionally relevant sites Biological RoleMethylated
cytosine(meC)
CpG islands Transcriptional Repression
Acetylated lysine (Kac)
H3 (9,14,18,56), H4 (5,8,13,16), H2A, H2B
Transcriptional Activation
Phosphorylated serine/threonine
(S/Tph)
H3 (3,10,28), H2A, H2B Transcriptional Activation
Methylated argine (Rme)
H3 (17,23), H4 (3) Transcriptional Activation
Methylated lysine (Kme)
H3 (4,36,79)H3 (9,27), H4 (20)
Transcriptional Activation
Transcriptional Repression
Ubiquitylated lysine(Kub)
H2B (123/120)H2A (119)
Transcriptional Activation
Transcriptional Repression
Sumoylated lysine (Ksu)
H2B (6/7), H2A (126) Transcriptional Repression
Chromatin modifications
Genome-wide Distribution Pattern of Histone Modification Associated with Transcription
Li et al. Cell (review) 128, 707-719Source: Li et al. Cell (Review, 2007), 128:707-719
EpigeneticsModifications of DNA (cytosine methylation) and proteins (histones) define the epigenetic profile.
In 1942, Conrad Waddington first used “epigenetics” to describe the interactions between genome and environment that give rise to differences between cells during embryonic development.
Currently, Epigenetics is the study of heritable changes in gene function that occur without a change in DNA sequence.
Summarizes mechanisms and phenomena that affect the phenotype of a cell or an organism without affecting the genotype.
Epigenomics is the study of these epigenetic changes on a genome-wide scale.
Normal Cellular Functions Regulated by Epigenetic Mechanisms
Correct organization of chromatin Genomic imprintingSilencing of repetitive elementsX chromosome inactivation
X-chromosome Inactivation
Source: Jones et al. Nat.Genet. 19, 187 (1998)
X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in female mammals is inactivated.
The inactive X chromosome is silenced by packaging in repressive heterochromatin.
The choice of which X chromosome will be inactivated is random in higher mammals such as mice and humans. Once an X chromosome is inactivated it will remain inactive throughout the lifetime of the cell.
Silencing initiated at Xic/XIC and spreads along chromososme.
5meC CpG DNA modification is observed in inactivated X chromosomes.
5meC binds transcriptional repressor MeCP2 (MethylC-binding Protein-2).
MeCP2 binds Sin3 with RPD3 histone deacetylase.transcriptional repressor
Histone DeacetylaseSin3
RPD3
MeCP25’..pCpGp..3’me
5
3’..pGpCp..5’5me
co-repressor
Epigenetic Diseases
Some human disorders such as Angelman syndrome and Prader-Willi syndrom are associated with genomic imprinting.
Involvement in cancer and development abnormalities.
The emerging hypothesis of cancer stem cells (CSC).
DNA Methylation and Gene Silencing in Cancer Cells
1 32 4
1 2 3 4
X
CGCG CG CG CG MCG
MCGNorma
l
Cancer
CG CG CGMCG
MCG
MCG
MCG
C: cytosinemC: methylcytosine
CpG island
Normal Cancer
Region-Specific Hypermethylatio
n
Accumulation of
Epigenetic Abnormalities
Global Hypomethylation
+
Progressive Alterations in DNA Methylation in Cancer
DNMT
Histone-modifying Proteins
Methyl-Binding Domain Proteins
Polycomb Repressors
Epigenetic Mediation of Gene Silencing
CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal
Normal Epithelia Dysplasia Carcinoma
in situ
Carcinoma
Metastasis
1
2
3
4
5
Normal Epithelia Dysplasia Carcinoma
in situ
Carcinoma
Metastasis
1
2
3
4
5
CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal
Normal Epithelia Dysplasia Carcinoma
in situ
Carcinoma
Metastasis
1
2
3
4
5
CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal
Normal Epithelia Dysplasia Carcinoma
in situ
Carcinoma
Metastasis
1
2
3
4
5
CpG Island Methylation: A Stable, Heritable and Positively Detectable Signal
Epigenetic Alterations in Cancer Stem Cells
Cancer Stem Cells: Stem cells arising through the malignant transformation of adult stem cells.
Cancer Stem Cells Hypothesis: Cancer stem cells are the main driving force behind tumor proliferation and progression.
Hallmarks of Cancer Stem Cells
A cell residing in a tumor that – 1. has a capacity to remain in an undifferentiated state 2. has properties of asymmetric divisions and self-renewal 3. has metastatic and repopulation capacities at specific niches
(microenvironment) in the body4. gives rise to a tumor that is histologically identical to the one
from which the CSC is derived
The Evidence of Cancer Stem Cells
First isolated from the patients of acute myeloid leukemia in 1997 by John Dick and colleagues at the University of Toronto.
Isolated from two solid tumors, breast and brain cancers.
~1% cancer cells may be really cancer stem cells.
More ChIP-chipStep 1: Rapid fixation of cells chemically cross-links DNA binding proteins to their genomic targets in vivo.
Step 2: Cell lysis releases the DNA-protein complexes, and sonication fragments the DNA.
Step 3: Immunoprecipitation (IP) purifies the protein-DNA fragments, with specificity dictated by antibody choice.
Step 4: Hydrolysis reverses the cross-links within the released DNA fragments.
Step 5: PCR amplification of ChIP DNA
Step 6: PCR amplification on a known binding-site region for that protein will need to be performed using either conventional PCR methods followed by agarose gel electrophoresis or by quantitative PCR.
Step 7: Labeling pool of protein-DNA fragments.
Step 8: Hybridization of DNA onto microarrays featuring 60-mer oligonucleotide probes.
Major types of array platforms
NimbleGen Arrays: tiling arrays, promoter arrays, whole
genome arrays.
(http://www.nimblegen.com/products/chip/index.html)
Agilent Arrays: promoter arrays, whole genome arrays.
(http://www.chem.agilent.com/Scripts/Phome.asp)
Affymetrix Arrays: tiling arrays, Chr21,22 arrays, whole
genome arrays.
(http://www.affymetrix.com/index.affx)
Measurement of intensity of probes on the array
The hybridized arrays were scanned on an Axon GenePix 4000B scanner (Axon Instruments Inc.) at wavelengths of 532 nm for control (Cy3), and 635 nm (Cy5) for each experimental sample. Data points were extracted from the scanned images using the NimbleScan 2.0 program (NimbleGen Systems, Inc.). Each pair of N probe signals was normalized by converting into a scaled log ratio using the following formula:
•Si = Log2 (Cy5l(i) /Cy3(i))
Confirming on a known target
Different antibodies to same factor
Antibodies to different family members
siRNA-ChIP
Antibodies to two components of a complex
Antibodies to an enzyme/modification pair
Antibody Validation
Confirming on a known target
Comparison of biological replicates and antibodies to different E2Fs
Loss of E2F6 ChIP signal after knockdown of E2F6 siRNA
•Promoter 1 •Promoter 2
Reproducibility of promoter arrays using biological replicates
•Top 1000 overlap
•Top 1000 overlap
•H3me3K27; Ntera2 cells
•500 kb region of chromosome 6
•500 kb region of chromosome 1
Amount of Sample Per ChIP
Number of cells Chromatin input
ChIP output
1x107 200 µg 150 ng
1x106 20 µg 10 ng
5x105 10 µg 1.3 ng
1x105 2 µg 300 pg
1x104 200 ng 30 pg
Amount of Sample Per ChIP
Number of cells Chromatin input
ChIP output
1x107 200 µg 150 ng
1x106 20 µg 10 ng
5x105 10 µg 1.3 ng
1x105 2 µg 300 pg
1x104 200 ng 30 pg
•Standard ChIP Protocol (1x107 cells; WGA2)
• Promoter Arrays
• Genome Tiling Arrays
•MicroChIP Protocol (10,000-100,000 cells; WGA4)
• Promoter Arrays
• Genome Tiling Arrays
Miniaturization
Reproducibility of MicroChIP Protocol