3. Chromosomes and epigenetics

Question 1

What are the three types of histone marks for gene expression regulation?

Answer 1

Closes chromatin:
- repressive (K9me, K27me)

Opens chromatin:
- enhancer (ac, K4me)
- promoter (K4me)

Question 2

Describe heterochromatin vs euchromatin

Answer 2

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)

Question 3

Explain the difference between facultative and constitutive heterochromatin

Answer 3

Heterochromatin types:
- Facultative: euchromatin that is silenced
- Constitutive: actually heetrochromatin

Question 4

What is the basic chromatin packing unit?

Answer 4

Nucleosome - bead wrapping 146 bp DNA around histone octamer + H1 linker histone => chromatosome structure

Question 5

What are the structures that can be formed by a poly-nucleosome?

Answer 5

Nucleosomes “beads on a string” accessible -> +H1 linker less accessible:
- clutches
- zigzags

Question 6

What part of nucleosomes is modified in changing chromatin states?

Answer 6

Histone tails (N-, C-termini) - protruding from nucleosomes - modified by PTMs - determine chromatin states

Question 7

What are the different modifications that change chromatin states?

Answer 7

Modifications changing chromatin states:
- acetylation
- methylation (supressor: H3 K9me, K27me; activating H3 K4me)
- phosphorylation
- ubiquitination

Question 8

What are the three enzymes that change histone modifications?

Answer 8

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

Question 9

Explain how histone acetylation acts on DNA accessibility

Answer 9

Activating: neutralizes lysine’s (K) pos charge - weakens interactions between histones - loosens chromatin

Acetylations added by HATs (writers) and removed by HDACs (erasers)

Question 10

Explain how histone methylation acts on DNA accessibility

Answer 10

Activating: H3 K4me
Repressing: H3 K9me, K27me

Lysine / arginine methylated -CH3 (mono / di / tri)

Question 11

What technique is used to detect specific chromatin modifications?

Answer 11

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

Question 12

Explain ChIP PCR technique

Answer 12

ChIp-qPCR - amplify the sequence

Question 13

Explain ChIP-seq technique

Answer 13

ChIP-seq - identify the sequence

Question 14

What are the three types of histone changes associated with change in gene expression?

Answer 14

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)

Question 15

How is specificity achieved for kinetochore assembly?

Answer 15

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

Question 16

What is position effect variegation (PEV) in Drosophila?

Answer 16

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

Question 17

What can manage variegation gene moving?

Answer 17

Supressor of variegation genes Su(var) - doesn’t let w+ jump into heterochromatin - red eyes

Question 18

In which part of chromosome DNA sequence is most similar within species?

Answer 18

Centromeres: most eukaryotic centromoeres share common chromatin structure but centromeric DNA is mostly species specific

Question 19

What is the effect of CpG dinucleotide methylation?

Answer 19

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

Question 20

How is X chromosome gene dosage achieved in female mammals?

Answer 20

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)

Question 21

Quiz 1

Answer 21

Question 22

Quiz 2

Answer 22

Question 23

Quiz 3

Answer 23