Term
| What enzyme methylates lysines? |
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Definition
| HKMT - histone lysine methyltrransferase |
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Term
| What lysine methylations are associated with active gene expression? |
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Definition
| Di and tri methylations of H3K4, H3K79 and trimethylation of H3K36 |
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Term
| What lysine methylations are associated with inactive gene expression? |
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Definition
| Di and trimethylation of H3K9 and K27 |
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Term
| Which domain of HKMT is catalytically active and what does it use to provide methyl groups? |
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Definition
| SET domain, S-adenosyl-L-methionine |
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Term
| Why is it thought that methylation changes gene expression? |
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Definition
| It creates motifs which other proteins act on |
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Term
| What is methylation of arginenes done by and what is it associate dwith? |
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Definition
| PRMTs- protein arginine methyltransferases, can be mono or di, can be inactive or active depending on residue |
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Term
| What is phosphorylation of serines and threonines associated with? |
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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). |
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Term
| What do mono and polyunbiquitylation do? |
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Definition
| Mono affects function, poly targets to proteasome, makes it a target for degradation |
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Term
| What does the chromodomain recognise? |
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Definition
| chromatin with H3 K9 and K27 methylation (associated with repressed chromatin) |
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Term
| What does Swi/Snf do and how? |
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Definition
| Slides nucleosomes along chromsomes to new positions - uses energy of binding beads to disrupt histone-DNA interactions |
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Term
| Eukaryotic genome is organised in chromatin loops tethered at the base by specific proteins - what do these loops represent |
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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 |
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Term
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Definition
| Loops associate together to form a series of domains in nucleus – occupy own space called territories (not all at random or mixed). |
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Term
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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. |
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Term
| What are eRNAs and what do they do? |
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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. |
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Term
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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. |
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Term
| How do lncRNAs silence transcription? |
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Definition
| lncRNA associates with silencing complex, targets silencing region of genome, H3K27 methylation and heterochromatin formation, heterochromatin inhibits gene transcription. |
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