L6 : Histone Code Flashcards
What is chromatin?
At simplest level, double stranded helical structure
DNA complexed with histones to form nucleosomes
What proteins make up the histone core?
H2A, H2B, H3, H4 comprise nucleosome core
- Each protein repeated twice, forming octamer
- DNA wraps around 1.65 times
- Histone tails stick out so available for modification
Note: H1b links individual nucleosomes together
What are the 4 main types of histone modifications?
- Acetylation
- Methylation
- Phosphorylation
- Ubiquitination
- Mostly Lys (K) is modified through acetylation and methylation
- Histone H3 Nt most commonly modified
- Globular region can be modified but not very accessible as buried
What are 3 minor types of histone modification?
- SUMOylation (small Ub-like modifier protein)
- Likely transcriptionally repressive - Biotinylation
- Addition of biotin
- Enriched in transcriptionally silent chromatin - ADP polyribosylation
- Addition of ADP-ribose polymers
- Maintains unmethylated CpG islands
What is histone acetylation?
Covalent reversible addition of acetyl groups from acetyl CoA to specific histones
How does acetylation affect transcription?
Usually stimulates transcription, indicator of gene expression
Predominantly occurs on H3 and H4
- H3K9, H3K14, H3K18
- H4K5, H4K8, H4K12, H4K16
- H2A and H2B can also be acetylated
What enzymes are involved in histone acetylation?
Acetyltransferases (HAT)
- Activation of transcription
- Families: MYST, GNAT, p300
Histone deacetylases (HDAC)
- Repression of transcription
- Families: I-IV
Why does histone acetylation allow for transcription?
- In unacetylated chromatin, positively charged tails interact with negatively charged DNA
- Acetylation of the tails weakens interactions, permitting TFs to bind DNA
- Neg acyl group neutralises pos lysine
Which domains recognise acetylated histones?
Bromodomains
- Recognise a short sequence of 4 AA (including acLys)
- Target specificity must depend on interactions with other regions
What is histone methylation?
Addition of methyl groups from S-adenosylmethionine (SAM) donor to histone tails
Can be mono-, di-, tri- methylated
How does methylation affect transcription?
Can indicate active or inactive chromatin
- H3K4, H3K36, H3K79 considered activating modifications
- H3K9, H3K27, H4K20 considered inactivating
What enzymes are involved in histone methylation?
Histone methyltransferase (HMT)
- SET domain is catalytic subunit responsible for transfering methyl
- HKMTs (H-Lys-MTs)
Histone demethylases
- Example PHF8
Which domains recognise histone methylation?
Chromodomains
- Effector proteins bind methyalted Lys via different conserved domains
- Chromodomain is common protein motif of 60 AA
- Example: HP1 and PRC contain
Why does histone methylation affect transcription?
Recruits effector proteins to chromatin to modify histones
- Have enzymatic activities and can lead to chromatin remodelling
- Can have activating or repressing effect
- Does not change overall charge of histones
Vernalisation
EXPAND
What cellular processes is histone phosphorylation associated with?
Transcriptional regulation
Apoptosis
Cell cycle progression
DNA repair
Chromosome condensation
Developmental gene regulation
What is histone monoubiquitination?
Ubiquitin is highly conserved 76 aa polypeptide
Covalently attached by Ub ligase to proteins
Reversably removed by deubiquitinating peptidases (DUBS)
How does histone monoubiquitination affect transcription?
Ub at K119 of H2A
- Associated with gene silencing
Ub at K120 of H2B
- Transcriptional activation
- Found on all transcribed genes in eukaryotes
- Plays clear role in gene regulation
How are histone modifications transmitted through DNA replication?
- Parental chromosomes equally distributed through replicated DNA
- New nucleosomes incorporated near origin
- Readers recognise modified histones
- Writers copy modifications to unmodified histones
- Parental pattern of modification is retained in new chromatin
Note: heritability applies mostly to stably silenced modifications (important for preserving cell function and identity)
