Histones and transcription (2)

DNA in the form of a chromosome is…

not naked

DNA complex in the chromosome

Beads on a string→ 30nm nucleosome→ Chromatin loops→ Chromosome

Histones in the nuclosome complex (3)

H2, H3, H4

Heterochromatin/ Repressive chromatin

• Condensed

• Transcriptionally inactive region

• Can be constitutive (telomeres, centromeres) or facultative

Euchromatin

• Thread-like so uncondensed

• Transcriptionally active region

The MAT locus allows…

to control the mating type in yeast (switch)

Why must HMLα or HMRa be silenced for the yeast to mate?

Because otherwise the cells will be diploid α/a and can’t mate

How is the mating type chosen?

Depending on the silencer sequence in front of the locus that is active = heterochromatin formation

How do telomeres behave similarly to the HML and HMR locus in yeast?

They also have silencer sequences that halt cell division when the chromosome gets too short

Transcription factors (proteins) that a required for MAT locus silencing (3)

1. RAP1

2. SIR1

3. SIR2, 3 and 4

RAP1

Binds to DNA in the silencer/telomere sequences

SIR1

Binds the silencer sequence near the silent mating type loci (can’t put it anywhere) with RAP1

SIR2, 3 and 4

Bind to hypoacetylated histone tails (H3, H4) and recruit more (+ve feedback loop bc SIR2 is a deacetylase)

Rpd3p (and SIR2)

Histone deacetylases

Repressor domain (RD) with DBD=

Transcriptional repression through deacetylation= Rpd3p enzymatic action on histone’s N-terminal tails

Activator domain (AD) with DBD=

Transcriptional activation through hyperacetylation= Gnc5 enzymatic action (HAT)

Why does acetylation of histone tails allow transcription?

Bc it neutralizes electrostatic interactions (negativeDNA and positiveHistones) and permits complex formation

Why co-activator/repressor?

Bc they lack specificity

How is that specificity confered to them?

By the transcription factors (AD/RD+DBD)

Pioneer transcription factors

1. Have 2 HATs

2. Can interact with chromatin even in its consensed form + recruitment of co-activators/repressors

What modification of the histone tails allows transcription?

Methylation on H3 K4 (mono, di, tri)

What modification of the histone tails blocks transcription?

Methylation of H3 K9 (mono, di, tri)

ChIP

Used to determine regions of the genome (genes) that are affected by modified histone tails

Epigenetic traits

Characteristics transmitted regardeless of the DNA sequence itself (toxins)

Types of epigenetic traits (3)

1. Inactive X/histone marks (methylation (Xist))

2. Developmental restrictions (legs vs antennae (Polycomb))

3. Imprints/marks (DNA methylations)

Epigenetic writers

Enzymes that add the marks to histones or DNA

Epigenetic readers

Proteins that recognize the imprint/marks/modifications

Example of epigenetic reader AND writer in histones

HMT or histone methyltransferase by recognizing neighbouring naive histones

H3K9me3

Example of mark