L14+15 HISTONE N CHROMATIN Flashcards
(45 cards)
epigenetics
- Inheritance of pattern of gene expression and gene function
- not changing primary sequence of DNA
- inherited by cells after cell division
how epigenetics is regulated
done by histone modifications to change chromatin - can be inherited between daughter cells of mitosis
- also can be done by dna methylation to affect chromatin structure
chromatin role
Package and condense DNA into a small volume to fit into cell nucleus
tightly coiled to produce the chromatid of a chromosome
Regulate access of TFs and transcription machinery to DNA sequence during transcription
and replication
Lock-in patterns of gene expression levels - the transcription of mRNA and its translation into protein
contribute to Tissue-specific variation in gene expression - which parts of the genome are transcriptionally active
chromatin, chromatid and chromosome
In mitosis metaphase, chromatin condenses to form chromosomes which split into two identical strands called chromatids. Each chromatid then becomes a chromosome in each new daughter cell that is formed
smallest unit of chromatin
nucleosome -form when DNA wraps around histone proteins.
1.8 turns of DNA wrap around nucleosome core
length of chromatin fibre
30nm. Further condensation during mitosis
chromatins then become…
Chromatin fibre - nucleosome coil into 30 nm chromatin fibre
after this, Chromosome scaffold proteins provide higher order organisation
nucleosome structure
Five histone subunits at nucleosome core:
H1, H2A,H2B, H3 and H4
- an octameric structure
Nucleosome coreis assembled sequentially from 2x H2A-H2B dimers plus H3-H4 tetramer –
Histone H1 binds to the linker region
Matrix-attachment regions (MARs)
also known as Scaffold-attachment regions (SAR)
are anchored to the nuclear matrix and induce the radial loop of chromatin - influence arrangement of gene expression
2 forms of chromatin in interphase nuclei
highly condensed heterochromatin : INACTIVE chromatin(TF can’t access)
less condensed euchromatin : ACTIVE chromatin (open to TF influence and transcription machinery)
meaning of active chromatin
the chromatin of active genes/ genes being expressed
reason for 2 forms
to facilitate the desired or required changes in gene transcription - for CHROMATIN REMODELLING: changing structure and position of the nucleosomes
how chromatin remodelling is done
by Chromatin remodelling complexes e.g. SWI/SNF
Hydrolysis of ATP provides energy
change how tight the DNA is bound and location of nucleosome
Promotes the exchange of histones in nucleosomes
these movings in histone placement allow different areas of DNA to open and be accessible
histone modification
N-terminal tails of core nucleosome proteins (H2A, H2B, H3 and H4) modified
Acetylation of lysines:
- Histone acetyltransferase (HAT)
- Histone deacetylases (HDAC)
Methylation of lysines and arginines:
- Mono-, di- and tri-methyl derivatives are possible
- Specific histone methytransferases (HMT) and demethylases
Phosphorylation of serines and threonines
Ubiquitination of lysines
histone modification
Each nucleosome contains histones that are
potentially modified in a large number of different
ways.
modification can turn gene on or off.
Pattern of modification is duplicated during DNA
replication.
modification is inherited between cells following mitosis
HAT properties and effect on histone
histone acetyl transferase is
a CBP (CREB-binding protein) complex - transcriptional activator - the response of cAMP activation
hyperacetylation of histones leads to active /open chromatin - active genes
hyperacetylation of histone effects:
induces nucleosome to bind to the DNA less tightly.
Lysine is positively charged. Acetylation changes charge of lysine. DNA is negatively charged and bound to lysine. Acetylation induces DNA to be less tightly bound = gene turned on.
Removal of acetyl group allows the same lysine to be methylated instead
leading to condensation and inactivation of chromatin = repression - transcription off
H3K9ac – activation
H3K9me - repression
drug target example
changing gene expression is a significant drug target.
SAHA - HDAC inhibitor
Binds to the active site of HDAC and chelates zinc ions involved in the enzyme reaction
Inhibits the removal of acetyl groups and chromatin remains in open state – genes stay active
histone methylation
unlike acetylation, methylation does not affect the charge of the amino group
methylation can induce active or inactive chromatin - dependent on lysine being methylated
Trithorax group (trxG) proteins methylates H3 lysine 4 (H3K4) = active chromatin
Polycomb group (PcG) proteins methylates H3 lysine 9 (H3K9) = inactive chromatin
DNA methylation - how
methylate (5’-methyl cytosine), ~5% bases mostly found in CpG dinucleotides
Hyper-methylation of CpG islands located at promoters linked with inactive chromatin
done by DNA methyltransferase (DNMT1, DNMT2, DNMT3).
enzymes transfer methyl group.
affects chromatin structure
DNA methylation - why,how and disorder
one of the epigentic contributions in controlling
tissue gene expression.
methylation of cpgs is inherited - maintained during DNA replication
Methylated CpG binds to MeCP2 (methyl CpG binding Protein 2)
MeCP2 recruits HDAC which leads to inactive chromatin
Mutation in MeCP2 gene causes neurodevelopmental disorder Rett syndrome
drug affecting gene expression example
5-azacytidine is a cytidine
analogue – gets
incorporated into DNA but
cannot be methylated.
for prevention of tumours becoming resistant to chemotherapy , due to a gene expression epigenetic change
X-chromosome inactivation
At fertilization female cells 2 X chromosomes are active
50% cells active maternal and 50% cells active paternal X
This is due to Xist - non coding RNA
Xist binds to Inactive X chromosome to trigger whole chromosome inactivation and to turn chromosome into heterochromia.
Xist recruits polycomb group methylases
inactive X chromosome is fully condensed as chromatin. it can be identified as so-called the Barr body - a very condensed X chromosome that doesn’t change during the cell life cycle.
Xist is 17kb transcript expressed from inactive X gene
Genomic imprinting
Normally, Diploid cells two alleles are both active for genes on autosomes (non-sex chromosomes)
Some genes are imprinted - one allele is repressed/ methylated, while the active allele is unmethylated.
Parental origin of a region of chromosome/ gene determines which gene is active
E.g. Insulin-like growth factor 2 (IGF2) only expressed from
paternal allele. only this locus of chromosome is imprinted
Epigenetic regulation is fixed due to parental origin.
Mutations can affect the epigenetic modification of imprinted genes e.g. Angelman syndrome and Prader-Willi syndrome
