Epigenetics

Question 1

Epigenetic modifications

Answer 1

Modifications of DNA by methylation
Modifications of histones
Assembly of protein structures on DNA

Epigenetic effects are mitotically heritable
Lead to heterochromatin (inactive) or euchromatin (active)

Question 2

Heterochromatin

Answer 2

Highly condensed
Transcriptionally repressed
May be constitutive (all cells the same) or facultative (varies between cells, X inactivation)

Question 3

CpG methylation

Answer 3

De novo methylase (DNMT3a/b) adds Me to one strand
Hemi-methylated DNA recognised by maintenance (perpetuation) methylases (DNMT1) which add Me to other strand
Demethylases remove methyl groups

Question 4

CpG islands

Answer 4

Methylation status regulates transcription
Islands located in promoter regions of constitutively expressed genes
Genes expressed when not methylated

Question 5

Modification of histones

Answer 5

Histone tails interact with other nucleosomes to compact DNA

Amino acids in tails can be modified to alter chromatin structure and function

Question 6

Histone writers, readers and erasers

Answer 6

Writers add modifications (histone acetyl transferase)
Readers are proteins that interact with modifications
Erasers remove modifications (histone deacetylase)

Question 7

Heterochromatin formation

Answer 7

Coupling of modification events
Histone deacetylase (eraser) removes Ac from H3K14
SUV39H1 (writer) tri-methylates H3K9
Heterochromatin protein 1 HP1 (reader) binds H3K9me3
HP1 drives heterochromatin formation

Question 8

HP1

Answer 8

Chromodomain containing protein
Chromodomains bind to specific methylated lysines
HP1 chromodomain binds di/tri-methylated H3K9

Question 9

Protein structure assembly on DNA

Answer 9

Polycomb group (Pc-G) proteins maintain repressed state
Perpetuate repression through cell divisions

Question 10

Pc-G proteins

Answer 10

Form complexes at polycomb response element (PRE)
PRE provides nucleation centre for complex binding and repression spread either side of PRE
Polycomb repressive complex 2 (PRC2) trimethylates H3K27 (writer)
PRC1 binds H3K27me3 and monoubiquitinates histone H2A on lysine 119 (reader and writer)

Question 11

X inactivation

Answer 11

Inactive chromosome is facultative heterochromatin
One chromosome inactivated at random
Depends on X inactivation centre (Xic)

Question 12

Xic

Answer 12

X chromosome counting and inactivation
Inactivation spreads from Xic along the chromosome
Xist coats X chromosome and recruits polycomb complexes
In active X, xist mRNA is negatively regulated by antisense Tsix