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Gene Regulation - Lecture 4
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16
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Undergraduate 3
01/14/2018

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Term
What enzyme methylates lysines?
Definition
HKMT - histone lysine methyltrransferase
Term
What lysine methylations are associated with active gene expression?
Definition
Di and tri methylations of H3K4, H3K79 and trimethylation of H3K36
Term
What lysine methylations are associated with inactive gene expression?
Definition
Di and trimethylation of H3K9 and K27
Term
Which domain of HKMT is catalytically active and what does it use to provide methyl groups?
Definition
SET domain, S-adenosyl-L-methionine
Term
Why is it thought that methylation changes gene expression?
Definition
It creates motifs which other proteins act on
Term
What is methylation of arginenes done by and what is it associate dwith?
Definition
PRMTs- protein arginine methyltransferases, can be mono or di, can be inactive or active depending on residue
Term
What is phosphorylation of serines and threonines associated with?
Definition
the change of modifications at adjacent sites
E.g phosphorylation of H3 T11 (associated with chromatin of active genes) promotes demethylation of K9 and acetylation of K9 and K14 (changes inactive-active).
Term
What do mono and polyunbiquitylation do?
Definition
Mono affects function, poly targets to proteasome, makes it a target for degradation
Term
What does the chromodomain recognise?
Definition
chromatin with H3 K9 and K27 methylation (associated with repressed chromatin)
Term
What does Swi/Snf do and how?
Definition
Slides nucleosomes along chromsomes to new positions - uses energy of binding beads to disrupt histone-DNA interactions
Term
Eukaryotic genome is organised in chromatin loops tethered at the base by specific proteins - what do these loops represent
Definition
each loop represents a domain containing active or repressed genes. Each is separate so actions to one loop (e.g. enhancers, silencers) doesn’t affect the next – insulated neighbourhoods. Insulator forms base of loop, can block the effects of enhancer if between enhancer and promoter = no transcription
Term
What are territories?
Definition
Loops associate together to form a series of domains in nucleus – occupy own space called territories (not all at random or mixed).
Term
What are TADs?
Definition
Loops vary in size, associate within the territories to form topologically associated domains (TADs). Each TAD has multiple chromatin loops. Different sized loops are tethered by different combinations of CTCF, cohesion and mediator complex.
Term
What are eRNAs and what do they do?
Definition
short, bidirectional RNAs transcribed by RNAp2 from gene enhancers. Presences correlates with promoter activation and requires presence of nearby promoter. Not part of gene – transcribed from DNA to regulate promoter, has roles in activating the nearby promoters – important to render the enhancer functional - short RNA transcribe to the enhancer or to make RNA, cut off or enhance promote, make enhancer more functional.
Term
What are lncRNAs?
Definition
long non-coding RNAs Some lncRNA (like XIST - X inactivation) bind to chromatin to modify complexes and probably produce their effects via chromatin structure – can activate as well as silence transcription.
Term
How do lncRNAs silence transcription?
Definition
lncRNA associates with silencing complex, targets silencing region of genome, H3K27 methylation and heterochromatin formation, heterochromatin inhibits gene transcription.
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