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25 Cards in this Set
- Front
- Back
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What enzymes does ATP-dependent chromatin remodelling require?
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Requires the enzymes of the SWI2/SNF2 ATPase superfamily. Subfamilies = SWI2/SNF2, ISWI, CHD/MI2, Ino80 All have SNF2-related ATP-ase. |
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What are the different things APT-ase can do to chromatin? |
Sliding Unwrapping Eviction Spacing Histone variant exchange |
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How does SWI/SNF remodel chromatin? |
Catalytic subunit of SWI/SNF = SNF2 (related to DNA helices but doesn't unzip - it twists and pushes) It hydrolyses 1000 ATP molecules per minute in the presence of DNA or nucleosomes. |
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What is SNF2? |
It is a molecular motor that uses energy from ATP hydrolysis to track along DNA and induce torsion (twists and pushes DNA). Results in disruption of histone-DNA interactions and movement of the nucleosome (position of binding sites moved). Bulge translocates around nucleosome so the binding site is now available. |
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What are the two related human complexes of SWI/SNF? |
hBRM and BRG1 |
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What are human SWI/SNF hBRM and human SWI/SNF BRG1 needed for? |
General transcription: for a number of transcription factors (glucocorticoid and retinoid receptors, HS factor, MyoD) |
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What are the roles of human SWI/SNF hBRM and human SWI/SNF BRG1? |
Roles in cell cycle control, development (deletion results in embryonic lethality), tumour suppressor pathways (deletion associated with a variety of tumour types) |
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How are SWI/SNF related to cancer? |
They are potent tumour suppressors but if mutated this can lead to cancer. |
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Do ATP-dependent and HAT complexes work synergistically? |
Yes, they are commonly recruited to the same promoters. Eg/// SWI/SNF and GCN5 regulate the same genes in yeast. |
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What is transcriptional repression mediated by? |
The recruitment of chromatin modifying factors: Histone Deacetylases (HDACs) ATP-dependent remodellers Histone Methylases (heterochromatin) |
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Are active regions of the genome hyperacetylated or hypoacetylated? |
Hyperacetylated Repressed regions are hypoacetylated. |
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What is histone deacetylation mediated by? |
HDACs |
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What do HDACs function as (like HATs functioned as co-activators)? |
Co-repressors |
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What are the 4 main groups of HDACs? |
Class l Class ll Class lV Class lll Class l, ll and lV are classical HDACs (zinc dependent) Class lll is part of the Sir2 family (sirtuins) - require NAD as a co-factor. |
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Where are HDAC co-repressor complexes recruited to and what is an example of this? |
Recruited to promoters by interaction with site-specific DNA binding proteins. An example of this is Sin 3 co-repressor: 1) Ume6 is a repressor that has a DNA binding domain (repression domain). 2) It interacts with Sin3 protein via Rpd3 as the catalytic subunit. 3) Sin3 is a structural protein that mediates the recruitment of the complex. 4) Ume6 brings HDAC to a specific promoter to mediate deacetylation. on N-terminal tails in the vicinity. 5) Set up repressive chromatin by deacetylating histone tails. |
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Do some ATP-dependent chromatin remodellers mediate repression? |
Yes. For example, the NuRD complex which belongs to the Mi2/CHD family. |
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What has the misregulation of NuRD complex been involved with? |
Misregulation shown to cause tumourogenesis. Several oncogenic transcription factors have been shown to recruit the NuRD complex to suppress the transcription of tumour suppressor genes. |
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What does NuRD do to cause transcription to be turned off? |
NuRD/NURF spaces the chromatin very tightly which causes transcription to be turned off. Slides nucleosomes together: Closed chromatin = transcription off Open chromatin = transcription on. |
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What are the 2 basic types of chromatin? |
1) Euchromatin (gene rich, potential to be transcribed) 2) Heterochromatin (gene poor, repetitive regions, transcriptional silencing, eg/// centromeres and telomeres) |
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What are the biochemical features of heterochromatin? |
1) Hypoacetylation 2) Specific histone H3 methylation (Lys9 and Lys27) 3) Association of specific silencing factors. |
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What is the process of the assembly of H3Lys9me heterochromatin? |
1) Removal of any acetyl groups on Lys9 of H3. This is done by HDACs. 2) Suvar 39 is a histone methyl transferase that methylates lys9 (mono, di or tri methylated). 3) Methyl mark acts as a beacon for the recruitment of the silencing factor HP1. 4) HP1 recognises modification and is assembled. |
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What is HP1? |
Heterochromatin protein 1 It is a chromodomain protein, these often recognise and bind to methylated lysine resides. The chromodomain of HP1 is specific for H3 Lys9me. |
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How can we use silencing assays to analyse heterochromatin? |
1) Normal wild type with ade6 euchromatin and heterochromatin centromeric repeats =ade6 gene expressed - white colonies. 2) Silencing reporter assay/strain where ade6 is inserted in middle of heterochromatic centromeric repeats = heterochromatin spreads across ade6 and switched it off, ade6 silenced - red colonies. |
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What is the process of heterochromatin: X-chromosome inactivation? |
1) At early development, embryonic stem cells are both active (X-chromosome). 2) Xic causes one to be inactivated. Xic contains 2 non-coding RNAs - Xist (forward) and Tsix (backwards). 3) In early development, both X-chromosomes are expressing Tsix. 4) Tsix inhibits the forward transcript Xist. 5) Later in development, Xist becomes unregulated (only in one X chromosome). 6) Xist coats the chromosome and recruits H3K27 methylase. 7) This leads to the recruitment of further silencing factors turning it off = INACTIVE X (Xi). 8) The chromosome that continues expressing Tsix = ACTIVE X (Xa) |
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What is an inactivated chromosome called? |
Barr body |
