3. Chromosomes and epigenetics Flashcards
What are the three types of histone marks for gene expression regulation?
Closes chromatin:
- repressive (K9me, K27me)
Opens chromatin:
- enhancer (ac, K4me)
- promoter (K4me)
Describe heterochromatin vs euchromatin
Heterochromatin: closed, gene poor, replicated in late S phase => the genes that are not expressed in that cell type (constitutive heterochromatin)
Euchromatin: open, gene rich, replicated in early S phase => genes specific for the specific cell type
-> small part of euchromatin actually expressed because: majority silenced (facultative heterochromatin)
Explain the difference between facultative and constitutive heterochromatin
Heterochromatin types:
- Facultative: euchromatin that is silenced
- Constitutive: actually heetrochromatin
What is the basic chromatin packing unit?
Nucleosome - bead wrapping 146 bp DNA around histone octamer + H1 linker histone => chromatosome structure
What are the structures that can be formed by a poly-nucleosome?
Nucleosomes “beads on a string” accessible -> +H1 linker less accessible:
- clutches
- zigzags
What part of nucleosomes is modified in changing chromatin states?
Histone tails (N-, C-termini) - protruding from nucleosomes - modified by PTMs - determine chromatin states
What are the different modifications that change chromatin states?
Modifications changing chromatin states:
- acetylation
- methylation (supressor: H3 K9me, K27me; activating H3 K4me)
- phosphorylation
- ubiquitination
What are the three enzymes that change histone modifications?
Enzymes involved in histone modifications:
- writers - adds modification
- readers - reads the signal of the modification
- erasers - removes the modification
Don’t directly read DNA - recruited by TFs or transcriptional machinery
Explain how histone acetylation acts on DNA accessibility
Activating: neutralizes lysine’s (K) pos charge - weakens interactions between histones - loosens chromatin
Acetylations added by HATs (writers) and removed by HDACs (erasers)
Explain how histone methylation acts on DNA accessibility
Activating: H3 K4me
Repressing: H3 K9me, K27me
Lysine / arginine methylated -CH3 (mono / di / tri)
What technique is used to detect specific chromatin modifications?
Chromatin immunoprecipitation (ChIP):
restriction of genome - using specific Abs for specific modifications on histone tails - based on Abs separate from the whole genetic mixture- identify:
- types of modifications present
- quantities of each modification
=>
ChIp-qPCR - amplify the sequence
ChIP-seq - identify the sequence
Explain ChIP PCR technique
ChIp-qPCR - amplify the sequence
Explain ChIP-seq technique
ChIP-seq - identify the sequence
What are the three types of histone changes associated with change in gene expression?
Histone changes that influence gene expression:
- histone modifications (ac, me, ph, ub)
- histone re-modelling (displacing nucleosomes)
- variant histones (diff histone versions - ex CENPA for kinetochore binding)
How is specificity achieved for kinetochore assembly?
DNA sequence not enough to determine kinetochore binding site - centromere chromatin contains CENP-A histones flanked by pericentromeric heterochromatin
CENP-A variant of H3 (60% sequence similarity) - conserved across species
What is position effect variegation (PEV) in Drosophila?
Variegation - state of having different colours
Position effect - where the gene for specific phenotype is - if accidentally moves from euchromatin to heterochromatin => position effect on variegation
Ex: PEV in Drosophila eyes - w+ (red) colour gene in euchromatin close to the end - mutagenesis induced - chromosomal inversion - w+ moves into heterochromatin - silenced in individual cells => loss of phenotype -> variegated eyes
What can manage variegation gene moving?
Supressor of variegation genes Su(var) - doesn’t let w+ jump into heterochromatin - red eyes
In which part of chromosome DNA sequence is most similar within species?
Centromeres: most eukaryotic centromoeres share common chromatin structure but centromeric DNA is mostly species specific
What is the effect of CpG dinucleotide methylation?
CG dinucleotide methylation - repressive + heritable epigenetic mark:
- high CG content: hypomethylated - open
- low CG content: hypermethylated - closed
Unmethylated CG dinucleotides organised in CpG islands - open - proteins that recognize methyl / unmethylated CpGs - can recruit complexes to maintain repressive / activating histone modifications
How is X chromosome gene dosage achieved in female mammals?
By random X inactivation - gene dosage compensation - packed into facultative heterochromatin:
in early development X randomly chosen - maintained in clonal descendant cells (diff epigenetic marks in diff cell lineages within a female) - tortiseshell cats
Inactivation:
X inactivation centre (X-sit) has XIST gene - ncRNA expressed Xist coats X - CpG islands become methylated along all chromosome except Xist centre -> Barr body = inactivated X chromosome (Xi)
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