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MCG > LEC23: Basal & Regulated Transcription > Flashcards

LEC23: Basal & Regulated Transcription Flashcards

1
Q

what are the phases of transcription?

A

1) pre-initiation complex formation
2) initiation
3) elongation
4) termination

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2
Q

where/what is the core promoter?

A

a DNA sequence in immediate vicinity of +1 site

where RNA Pol II binds, directed by other protein factors

may contain “consensus” sequence - similar sequence found in promoter regions of many genes

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3
Q

how are upstream ntds designated from txn start site?

A

negative numbers

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4
Q

where is the TATA box located re: +1 site?

A

-20 - -30

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5
Q

what are TFIIs?

A

transcription factors for RNA Pol II

bind DNA, and each other, to direct localization of RNA Pol II for initiation of txn at +1

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6
Q

what is TFIIH kinase?

A

a **ser-thr kinase, one **of the transcription factors for RNA pol II

**phosphorylates **the **CTD **of RNA Pol II, & this signals to being transcription

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7
Q

what is the CTD?

A

C-carboxy-terminal domain of one of the RNA Pol II subunits

has many Ser-Thr residues

gets phosphorylated by TFIIH kinase - **this is the signal to begin transritoin **

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8
Q

what begins txn initiation?

A

TBP, TATA box binding protein, binding

results in bending of the DNA

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9
Q

what is the signal to begin txn?

A

phosphorylation of the Ser-Thr residues of the CTD of one of the RNA Pol II subunits

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10
Q

what does the TFIID complex consist of?

A

TBP and many TAFs, TBP-associated factors, and TFIIs (A, B, D, F, H), and mediator

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11
Q

what is the pre-initiation complex?

A

complete ensemble of protein complexes at txn initiation sit,

TFIIs, TBP, Mediator, RNA Pol II

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12
Q

what is different between RNA and DNA polymerases?

A

RNA polymerase can start de novo; DNA polymerase cannot

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13
Q

what needs to happen so that elongation can begin?

A

PIC formation and binding to the txn initiation site, followed by

promoter clearance

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14
Q

what is the rate of txn elongation?

A

50 ntd/second

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15
Q

what happens once RNA Pol II complex leaves promoter region to transcribe downstream sequences?

A

another RNA Pol II complex can load right behind it, begin txn

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16
Q

what do helicase and topoisomerase do?

A

helicase: enzyme that unwinds the DNA helix; causes tension in helix; part of TFIIH complex

topoisomerase: alters topology of DNA dbl helix by cutting 1 strand of the tightly wound DNA dbl helix, relaxing helix, putting it back together again; relieves tension = crucial for elongation

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17
Q

what happens to phosphates on CTD at termination?

A

when RNA Pol II comes off the DNA template, a CTD phosphatase takes off the phosphates that were added to the CTD

**de-phosphorylate **when done w/ txn

now RNA Pol II transcribes again

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18
Q

what is the core promoter?

where is it re: +1 site?

what binds to it?

A

cis element where txn initiation factors bind

-40 to +40, in and around +1 site

TFIIs, mediator bind; but TFIIs may have protein-protein interactions to PIC rather than bind directly to the DNA

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19
Q

what are promoter proximal elements?

where are they?

what do they bind?

A

cis elements that are bound by unregulated txn factors

-40 to -200, close to core promoter

proteins that constituitively enhance the initiation of txn bind here

20
Q

what are enhancers?

where are they?

what do they bind?

A

100-500 bp long cis element of DNA where regulated txn factors bind

can be located anywhere! upstream, downstream, doesn’t matter

multiple txn factors bind to an enhancer to enhance the rate of txn initiation

21
Q

what % of our genome encodes for txn factors?

A

10%

22
Q

what are simple vs. complex enhancer sequences?

A

simple: multiple repeats of the same sequence, are bound by same txn factors

complex: different DNA boxes w/ different sequences can be bound by different txn factors

23
Q

what are the elements of a txn factor?

A

1) DNA binding domain: binds DNA, recognizes sequence; can be a zinc finger or helix-turn-helix

**2) activation domain: **talks to another protein to activate txn initiation rate

**3) dimerization domain: **allows formation of homo- or hetero-dimers (or tetramers) of txn factors

24
Q

how do txn factors bind?

what are some motif examples?

what does this kind of structure afford txn factors?

A

as dimers or tetramers

dimers increase txn factor diversity

leucine zipper, helix-loop-helix, zinc finger

25
Q

why is the # of txn factor complexes that can bind to enhancers and influence rate of txn >>> total # of txn factor proteins?

A

b/c they can bind as homodimers, tetramers, heterodimers; gives greater combination possibilities

26
Q

what can the txn factor activation domain interact w/?

A

1) directly w/ constituents of teh PIC to increase the rate of txn
2) w/ co-activators that change the state of local chromatin

27
Q

how does it work that enhancers can be very far away from promoter?

A

DNA loops; not concrete in shape

can have something v. far away, loops back on itself

txn factor binding on enhancer & the PIC as formed at promoter then get brought together

28
Q

if you had a mutation in TFIID, TBP, RNA Pol II, what would likely be result?

A

incompatible w/ life b/c so crucial to the basal txn of all genes, cannot form life

29
Q

where do we often see specific txn factors’ mutations?

A

diseases

i.e. P53: often mutated in cancer

30
Q

what enzymes can be recruited to enhancer sequence to modify chromatin?

A

1) histone modifying enzyme
2) chromatin remodeling complex

31
Q

what is histone acetyl transferase (HAT)

A

a histone modifying enzyme that acetylates histone lysine residues

this changes charge from (+) to neutral; reduces interaction btwn histone & DNA

this activity assoc w/ loosening of the histone-DNA interaction which we want for enhanced PIC formaiton, txn initiation

32
Q

what can reverse acetylation of histones?

A

HDAC, histone deacetylase

removes acetyl group from histone, restores positive charge to Lysine

restores chromatin structure

usually has inhibitory effect

33
Q

what is histone methylase, what does it do?

A

adds methyl group to epsilon amino; methylation of lysine group

changes chromatin confroamtion

can be up or down regulator of gene expression

34
Q

what does histone demethylase do

A

removes methyl groups added to chromatin by histone methylase

35
Q

what does histone kinase do

A

phosphorylates serine; gives it negative charge

opposite: histone phosphatase

also changes chromatin structure

36
Q

what does a chromatin remodeling complex do?

A

changes how nucleosome looks; doesn’t modify histone

37
Q

what are writers, erasers, readers, re: histone modifications?

A

writers: enzymes that put on histone marks
erasers: enzymes that take off histones
readers: recognize, modify histone; bind & do something to chromatin structure

38
Q

what is the histone code?

A

idea that there is some kind of code that’s read by the cell about state of histones, to either up/down regulate txn

39
Q

H3 histone modifications:

1) what does methylation of K9 do
2) what does methylation of K4+acetylation of K9 do?
3) what does phosphate on S10 and acetyl on K14 do?

A

1) heterochromatin formation, gene silencing
2) gene expression
3) gene expression

40
Q

what do chromatin remodeling complexes do?

A

change histone protein composition of the nucleosome or reposition nucleosomes on the DNA to expose regulatory sequences

usually involves multiple txn factors in regulation for a single gene

can: subtitue variant histones; move nucleosomes; move histone cores; reveal DNA that now can be accessed by another protein

41
Q

how many kinds of histones are there

A

mainly think of H2A, H2B, H3, H4, and H1, but know that **there are different subtypes of histones of the histone core of chromatin **and remodeling complexes can substitute variant histones, change chromatin structure, function

42
Q

what are epigenetic changes? how are they transmitted?

A

changes to chromatin that don’t change DNA sequence, but change what chromatin looks like

heritable changes via cell division across generations

43
Q

how can txn factors’ activity be regulated?

A

1) post-translational modification (i.e. MAPK pathway: ERK kinase P-lates a txn factor)
2) proteolysis: degredation of a txn factor
3) localization: i.e. NOTCH
4) ligand binding: txn factors need sthg to bind to it, activate
5) synthesis: need a txn factor’s gene to make it!

44
Q

where/what is a CpG island

A

high concentration of CG dinucleotide in a small sequence

typially, near promoter sequences

45
Q

what does DNA methyltransferase do?

what does it do to CpG islands? result?

A

enzyme that transfers a methyl group to DNA

happens to cytosine of CpG island

causes epigenetic change:

recruits **MeCP2, **methyl CpG binding protein 2: **represses txn **by recruiting a histone deacetylase

46
Q

how does Rett Syndrome occur?

A

knock out of 1 copy of MeCP2 gene

MeCP2 is on X chromosome

if have reduced MeCP2 expression, certain genes are expressed at higher level than they should be

MCG (77 decks)

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