Chromatin remodelling and modification Flashcards
why eukaryotic gene are off in ground state?
Heterochromatin: highly compressed and not transcribed
Regulatory elements is hidden from the regulatory gene
Chromatin structure can be altered by
– Histone protein tail acetylation
– DNA methylation
– SWI-SNF chromatin remodelling protein complex
Packaging of eukaryotic DNA into chromatin
– Regulatory sequences required for transcription
(promoter, promoter-proximal elements and
enhancers) are inaccessible for most of the
genes
Chromatin remodeling exposes regulatory sequence
Shifting of DNA along the nucleosome in such away where the promotor is exposed for regulatory protein binding
How does modification of histone effect gene expression?
Modification of histones (acetylation,
methylation) controls gene expression
via different mechanisms
Acetylation of histone tails
• Acetylation (CH3CO) of histone tails stops
interaction with neighboring nucleosome and DNA
Histone tails
• Histone proteins have amino acids “tails” which
stick out of the nucleosome
• The histone tails can bind next nucleosome and
adjacent DNA
– Favourable electrostatic interactions between Lys
residues of the tails (+) and:
• negatively charged pocket on the adjacent nucleosome
• negatively charged phosphate backbone of the surrounding DNA
– Stabilises condensed structure
De-acetylated histone tail
De-acetylated Favors condensation—> Represses transcription —> Gene inactive
positively charged tail is attracted to the negatively charged surface of histone
Positively charged tail is attracted to the negatively charged phosphate backbone of the DNA
Acetylated histone tail
Acetylated —-> Stops condensation—-> Favors transcription—-> Gene active
Acetyl removes the positive charge on the tail and become neutral —> nucleosome dissociates
Acetylation of histone
Reversible
• HAT = enzyme histone acetyltransferase
• HDAC = enzyme histone deacetylase
Regulation by histone acetylation
How does the level of acetylation effect the gene expression?
Level of histone acetylation affects gene
expression
– More acetylation = more transcription
– Less acetylation = less transcription
Regulation by histone acetylation
- increasing acetylation
Some eukaryotic activator protein complexes
direct acetylation of histones near promoters
– Opens chromatin structure and increases gene
transcription
Regulation by histone acetylation
- decreasing acetylation
• Some eukaryotic repressor protein complexes
direct de-acetylation of histones near promoters
– Compresses chromatin structure and reduces gene
transcription (as is the case for the yeast GAL genes
in the presence of glucose, the preferred substrate
what happens in presence of glucose and galactose to GAL gene expression?
In presence of galactose and glucose, the transcription of GAL1 is repressed regardless of presence of activator GAL 4 on the UAS
Mig1 repressor binds between UAS and promoter and recruits Tup1 that has an HDAC activity.
DNA becomes deacetylated in this region, turning the gene transcription off
Methylation of histone tail
Lysines and arginines
• HMTase = enzyme histone methyltransferase
• Does not affect the charge
• Creates binding sites for either activator or
repressor proteins
– Depends on the residues modified
• Can activate or repress gene expression
DNA methylation
where does it occur?
Covalent modification of DNA rather than histone
proteins
– 5’ position of cytosines
– DNA methyltransferase
– In mammals, it is usually the C of the CG dinucleotide
– C*G still capable of nucleotide pairing
70-80% of all CG dinucleotides are methylated
Effect of CG dinucleotide methylation
CG methylation is associated with inactive genes
– Unmethylated dinucleotides are found in clusters near
active promoters (“CpG islands”, p=phosphodiester
bond)
– Link between DNA methylation and transcriptional
repression by histone deacetylation
Link between DNA methylation and transcriptional
repression by histone deacetylation
Methylation of 5’ position of C –> (methyl sreves as a recognition site) methyl cytosine binding protein arrives –> Histone deacylase binds to the MeCP –> deacetylation of histone —> aggregation of nucleosome
The b-interferon enhanceosome
Multiple transcription factors control expression of b-interferon gene
– Required for defence against viral pathogens
• Binding of multiple regulators is co-operative
– Binding of first protein helps other proteins to bind and stabilises their binding
enhanceosome
enhanceosome helps recruits the transcriptional machinery
How TATA box is exposed?
Nuc 2 is strategically positioned over TATA box
and transcription start site
The enhacosome forms binding site for GCN5 (HAT) which binds and adds acetyl groups to Nuc 1 and Nuc 2
What happens after GCN5 dissociates?
GCN5 dissociates, a “landing pad” for coactivator
CBP is formed CBP recruits RNA polymerase II and SWISNF (“switch-sniff”) chromatin remodeling
complex
SWI-SNF is an ATP-driven molecular motor, it uses
the energy of ATP hydrolysis to nudge nuc2
of the TATA box, making it accessible to the TBP
The TBP binds to the newly exposed TATA box allowing transcription to begin
• Chromatin structure can be inherited
In DNA replication, BOTH DNA sequence and the chromatin structure are passed onto the next cell generation
• During replication, old histones are re-used by both daughter cells and serve as templates to guide the modification of new histones
DNA methylation pattern can also be inherited
In DNA replication, only the parental strand will be methylated
• DNA methyltransferase recognises these hemimethylated
substrates and methylates the other strand according to the
methylation pattern on the parental strand
