H6 Mosher- Chromatin structure and gene expression, including epigenetics

how do the different histone proteins assemble? how does this associate with DNA?

• conserved ‘histone fold’ shape- small helix-turn-large helix-small helix

• H2A and 2B form a dimer x 2

• H3 and 4 form a tetramer

• the histone octamer is one H3-H4 tetramer (binds to ~1 loop of DNA first) and two H2A-H2B dimers

• ~147 nucleotide DNA wraps around this core particle almost twice

• N-terminal histone tails extrude out from the DNA- can be modified for DNA marking

• H1 is the linker histone protein- this can bind the linker DNA (between two nucleosomes) and clamp the entry and exit DNA together for higher compaction eg. more abundant in heterochromatin

how do nucleosomes assemble?

• nucleosomes complexes on DNA take up a ‘beads on a string’ or 10nm fibre structure (when actively transcribed)

• this is assembled into a 30nm fibre (hypothesised by solenoid or zigzag structure)

• chromatin is bound to the nuclear matrix by proteins, to make chromatin loops (unknown how)

• within the interphase nucleus, the chromosomes have distinct territories because they stay bound to the matrix; they aren’t all intermixed

• this is compressed down further to produce meiotic/mitotic chromosomes

what is heterochromatin?

• some sections of chromatin, called heterochromatin, stain more densely/darkly than others, called euchromatin

• these are mostly distributed at the pericentromere, but can also have occasional knobs or blobs

• most genes are in the euchromatin, while the heterochromatin contains more ‘junk’ DNA eg. transposons, that the host doesn’t want to transcribe

• heterochromatin is resistant to gene expression

• we observe position effect variegation (PEV)- the position of a gene in a chromosome determines whether it is constantly or partially expressed

  • eg. the white gene in drosophila eyes causes red pigment to be produced, but when exposed to X-rays, inversions bring it into the pericentromeric heterochromatin

  • this suppresses white gene transcription, causing less red pigment to be produced = variegation

  • Su(var) genes encourage heterochromatin, decreasing transcription of the white gene so that variegation is increased (su(var)^- mutation suppresses variegation)

  • E(var) genes suppress heterochromatin

how is heterochromatin maintained, using the example of the drosophila white eye gene?

• the H3K4 demethylase Su(var) demethylates the lysine at position 4 in histone H3, which is otherwise a chemical marker for being euchromatin, as it recruits chromatin remodelers etc. (H3K4me and H3K9me are mutually exclusive)

• the H3K9 methyltransferase Su(var) methylates the lysine at position 9 in histone H3, which is a chemical marker for being heterochromatin

• two heterochromatin protein 1 Su(var)s recognise and bind two adjacent nucleosomes with H3K9me modifications, dimerise, and form a binding platform for effector proteins eg. HDAC:

• the histone deacetylase Su(var), HDAC, removes acetylation on lysine residues in histones (acetylation of positively charged lysine makes them neutral = weakened DNA ionic interactions)

• this increased positive charge tightens bonding with histones, maintaining heterochromatin

• maintaining heterochromatin = white⁺ gene transcribed less = less red pigment = more variegation

• Su(var)^- variants = decreased heterochromatin = white⁺ gene transcribed more = more red pigment = suppressed variegation

what are the structural and maintenance differences between heterochromatin and euchromatin?

heterochromatin:

• demethylation at H3K4

• methylation at H3K9 is bound by heterochromatin protein 1

• this is a binding site for histone deacetylase = condensed chromatin

• also has abundant H1 linker protein

• this leads to trasncription repression

euchromatin:

• methylation at H3K4

• demethylation at H3K9 = no HP1 binding = uncondensed chromatin

• also has low H1 linker protein

• this permits transcription

how is heterochromatin maintained in DNA replication?

• when DNA is unwound to create a replication bubble, the histones are evicted

• the H3-H4 tetramers are randomly transferred to either daughter strand (red)

• this dilutes the heterochromatin markers on H3 by 50%

• the newly-produced nucleosomes (grey) that are added are reinforced with markers by reader and writer domains