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cmb2001 > lecture 4 > Flashcards

lecture 4 Flashcards

1
Q

what are the post translational modifications of histones?

A

acetylation, methylation, ubiquitylation, phosphorylation

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2
Q

what are the post translational stages of modification?

A
  1. writing - add modifications
  2. erasing - remove modifications
  3. reading - proteins with these domains that regulate these modulated histones
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3
Q

what is the histone code?

A

different modifications constitue a code which dictates a transcriptional state of underlying DNA

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4
Q

what occurs in ATP-dependent chromatin remodelling?

A

-nucleosome is repositioned
-uses energy from ATP hydrolysis to promote different reactions with chromatin

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5
Q

what different reactions with chromatin are promoted?

A

sliding with nucleosome, unwrapping of DNA, space chromosomes neatly, promote histone variant exchange

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6
Q

what is responsible for spacing out nucleosomes?

A

ISWI

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7
Q

what are the properties of SWI/SNF?

A

-hydrolyses 1000 ATP molecules per minute
-related to DNA helicases
-molecular motor as uses energy from ATP hydrolysis to track along DNA and induce torsion
-disrupts histone

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8
Q

how doesSWI/SNF remodel chromatin?

A

-uses energy from ATP hydrolysis as molecular motor tracks along DNA and introduces torsion and twists
-causes disruption of DNA with the nucleosome
-effectively wraps the DNA around nucleosome
-location of binding site is moved

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9
Q

how do ATP-dependent and HAT complexes co-operate?

A

-commonly recruited to the same promoters
-remodel function together
-transcription factor binds to DNA and recruits acetyl histone transferase
-this acetylates nearby nucleosomes and brings about recruitment of SWI/SNF

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10
Q

what do bromodomains in Snf2 allow?

A

to tether it to acetylated nucleosomes

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11
Q

what are the functions of the SWI/SNF complex in yeast?

A

-general transcription

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12
Q

what are the 3 complexes in the SWI/SNF in humans?

A

PBAF, cBAF, ncBAF

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13
Q

what are the roles of these complexes?

A

-general transcription (needed for txn factors)
-cell control via interaction with Rb and cyclin E
-development
-role in tumour suppressor pathways

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14
Q

how is SWI/SNF linked with cancer?

A

-at least 9 different genes encoding SWI/SNF are recurrently mutated in cancer

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15
Q

what is the tumour suppressor activity of SWI/SNF likely to be because of?

A

-roles in facilitating transcription factor function

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16
Q

how is transcription repressed?

A

-mediated by recruitment of chromatin modifying factors
eg. histone deacetylases, ATP dependent remodellers, histone methylases (formation of heterochromatin)

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17
Q

which region is hyperacetylated?

A

active regions

18
Q

which regions are hypoacetylated?

A

repressed regions (low transcriptional activity, low acetylation)

19
Q

what is deacetylation mediated by?

A

histone deacetylases (HDACs)

20
Q

what are the 4 major groups of histone deacetylases?

A

class I, class II, class IV (all zinc dependent enzymes), class III (require NAD as cofactor)

21
Q

how do HDAC co-repressor complexes work????

A

-recruited to promoters by interaction with site specific DNA binding proteins (repressor proteins)
-deacetylation of N terminal tails
-UME6 repressor binds to upstream repressor sequence through binding domain
-regulatory domain interacts with sim3
-nucelosome is deacetylated to prevent proteins helping the PIC formation

22
Q

what commonly mediates transcriptional repression?

A

ATP-dependent remodellers

23
Q

what does closed chromatin mean?

A

transcription off

24
Q

what does open chromatin mean?

A

transcription on

25
Q

what are the two basic types of chromatin?

A

euchromatin and heterochromatin

26
Q

what are the properties of euchromatin?

A

-gene rich
-potential to be transcribed
-viewed as light stained through microscope

27
Q

what are the properties of heterochromatin?

A

-gene poor
-repetetive regions
-transcriptional silencing
-usually dark stained through microscope

28
Q

what are the biochemical features of heterochromatin?

A
  1. hypoacetylation - very low levels of acetylation
  2. specific histone H3 methylation
  3. association of specific silencing factors
29
Q

how is heterochromatin assembled?

A
  1. lysine 9 cant be acetylated (to form heterochromatin) so histone deacetylase needed to remove any acetyl groups associated with the molecule
  2. a histone methyltransferase called suvar39 methylates lysine 9 on histone H3
  3. this forms a docking site/assembly site for a component of heterochromatin
30
Q

what are the properties of heterochromatin protein 1?

A

-chromodomain
-can recognise methylated lysine
-forms pocket where lysine 9 fits (docking site)

31
Q

what does binding of HP1 cause?

A

-compaction of nucleosomal arrays
-acts as platform for recruitment of further activities that prevent recruitment of RNA pol II

32
Q

how does binding HP1 prevent recruitment of RNA pol II?

A

-HP1 has region that attracts other enzymes like histone deacetylases to ensure all histone tails are deacetylated

33
Q

how are reporter silencing assays used to analyse heterochromatin?

A

-reporter gene is located
-ade6 repressed

34
Q

what occurs in the ‘normal’ wild type?

A

-ade6 gene expressed
-white colonies

35
Q

what occurs in silencing reporter stain?

A

-ade6 silenced
-red colonies

36
Q

what occurs when the ade6 silencing is alleviated?

A

white/pink colonies

37
Q

what is controls Barr body formation?

A

-non coding RNAs Xist and Tsix
-regulate X chromosome inactivation

38
Q

what area drives X chromosome inactivation?

A

Xic

38
Q

what leads to the X chromosome being inactivated?

A
  1. in early development, both X chromosomes are making the tsix transcript
  2. later, one X chromosome represses tsix and instead upregulates the xist
  3. the other X chromosome continues to express tsix and becomes the active chromosome (lots of genes expressed)
  4. xist binds to x inactivation centre and coats the entire chromosome
  5. indirectly, xist recruits binding of xist and recruitment of a methylase which methylates h3k27 leading to chromodomain protein polychrome that silences expression from X chromosome
39
Q

what is the function of the tsix transcript?

A

prevents transcription initiation to drive formation of xist (an antisense transcript)

cmb2001 (10 decks)

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