L10 - Chromatin Structure and Gene Transcription Flashcards
Genetic alterations to DNA sequences
Permanently affect gene expression.
Epigenetic changes to chromatin structure
Modulate gene expression. Do not alter DNA sequence Are reversible Facilitate stable changes to gene expression which may persist for the life of a cell Can be erased in the germ line
What are nucleosomes?
Nucleosomes can be covalently modified.
N terminal lysine rich tails (8 of them) of core histones project radially from nucleosomal core.
Covalent modifications differ between condensed inactive and open active chromatin.
Types of covalent modification to core histone N-terminal tails
- Acetylation of lysines
- Methylation of lysines and arginine’s
- Methylation/acetylation to termini lysine and serine side chains
Histone acetyltransferases
Modify lysine residues
Histone code writers
Activates gene transcription
Histone methyltransferases
Exhibit site specificities
Histone code writers
Represses gene transcription
Histone deacetylases
Remove modification
Histone code erasers
Represses gene transcription
Histone demethylases
Remove modification
Histone code erasers
Activates gene transcription
Lysine and arginine methylation effects on gene expression?
- H3-K4 active
- H3-K9 inactive
- H3-K27 inactive
- H3-R17 active
Lysine acetylation effects on gene expression
- H2A active
- H2B active
- H3 active
- H4 active
What does acetylation of histones create binding sites for?
Transcription activators that contain a bromodomain
The bromodomain transcription activator is an epigenetic code reader
Mapping of histone acetylation across genes
Histone acetylation is associated with transcriptionally active promoter sequences
What does methylation of histones create binding sites for?
Transcriptional repressors that contain a chromodomain
Transcriptional activators that contain a PHD zinc finger domain
- Depends on the lysine amino acid residue modified
These are both epigenetic code readers
What is the transcriptional regulatory code?
An epigenetic code that lies on top of the genetic code
Governs when and where genetic information is expressed
How do transcription activator proteins work?
- Nucleosome remodelling
- Histone removal
- Histone replacement
- Histone modifications
- Recruitment of code writers and readers
Activator proteins
Typically induce combinations of these effects.
All the effects promote RNA polymerase II recruitment.
How do transcription repressor proteins work?
- Recruitment of chromatin remodelling complexes
- Recruitment of histone deacetylases
- Recruitment of histone methyltransferases
- Competitive DNA binding
- Masking activation surface
- Direct interaction with general transcription factors
What is the Polycomb Repressive Complexes?
Includes proteins that can generate or recognise repressive chromatin modification
- Histone code writing
- H3-K27 methylation
- Mediated by Enhancer of zeste (EZH2) component of PRC2
- Histone code reading
- Recruitment of PRC1 via Polycomb chromodomain
- Formation of silent, repressed heterochromatin
Relationship between transcriptionally repressive histone methylation and DNA methylation
Transcriptionally inactive promoters are rich in methylated CpG dinucleotides
Addition of methyl groups to cytosine residues is mediated by DNA methyltransferases (DNMTs)
Histone methyltransferase (EZH2) interacts with DNMTs and mutually reinforce their effects
Transcriptionally inactive promoters are rich in?
Methylated CpG dinucleotides
Addition of methyl groups to cytosine residues is mediated by?
DNA methyltransferases (DNMTs)
Mammalian X-chromosome inactivation
Equalises levels of X-chromosome derived gene products in males and females
- Males, XY - 1 dose of X-linked genes
- Females, XX - 2 doses of X-linked genes
Silencing of one X chromosome of female embryo during development
Initial selection of the chromosome for silencing is random
Silenced by condensation
The silencing decision is propagated clonally
- All progeny of cells in which the silencing occurred inherit the same silenced X chromosome
Calico cat is an example of?
X-chromosome inactivation
Mechanism of X-inactivation
- Xist RNA binds to the X chromosome in cis
- Promotes chromatin condensation –spreads away from x-inactivation centre in both directions
- Promotes formation of silent chromatin by recruiting histone modifying enzymes and other Polycomb group components
- Leads to H3K27 and H3K9 methylation of core Histones
- Leads to chromatin condensation and transcriptional repression inactive X
What is a Barr body?
A highly condensed inactive X chromosome at the periphery of the nucleus of female somatic cells
Polycomb proteins role
Detect Xist transcripts on the X chromosome that is to be inactivated
They cause its transcriptional silencing
Agouti mouse is an example of?
How dietary components can affect DNA methylation patterns which regulate phenotypes
Calico cat genes
Females: - XO XO : orange - Xo Xo: black - XO Xo: calico They are exclusively female They are heterozygous for 2 alleles of an X-linked coat pigment gene
Agouti mouse genes?
Agoutivy - dominant mutant allele
- Causes obesity and yellow fur
- Due to constitutively high expression of the agouti protein
- Contains an insertion of an IAP element - strongly activates the agouti gene
IAP element in Agouti mouse
IAP element is sensitive to DNA methylation
- High levels of methyl donors in maternal diet represses Agoutivy transcription in progeny
Increasing levels of methyl donor molecules in diet can?
Rescue the phenotypic effects of Agoutivy by increasing DNA methylation which represses transcription of the Agoutivy gene
Methylation and acetylation of some lysines are?
Mutually exclusive
Mechanism of X-inactivation
Involves synthesis of a non-coding RNA (Xist) from the X-inactivation centre (XIC) on the chromosome destined for inactivation
