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Genes, Genomes and Biomedical Implications > Specific Transcription Factors > Flashcards

Specific Transcription Factors Flashcards

1
Q

How to TFs bind to specific DNA sequences?

A

through their DNA binding domains

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2
Q

How do TFs interact with the basal transcription machinery?

A

through protein-protein interaction via their activation domains

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3
Q

What are the 2 techniques used to identify the binding site of DNA and TFs?

A
  • DNase I foot printing
  • EMSA
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4
Q

What part of DNA do TFs make the most contact with?

A

the major groove

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5
Q

How does DNA interact with proteins?

A
  • H bonds
  • ionic bonds
  • hydrophobic interactions
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6
Q

What does Asn have?

A

a side chain that directly interacts with the major groove of the DNA molecule

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7
Q

How are TFs classified?

A

based on their conserved DNA binding domains

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8
Q

What are the 4 main TF binding domains?

A
  • zinc finger
  • homeodomain
  • helix-loop-helix
  • leucine zipper
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9
Q

What does each TF control?

A

multiple genes

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10
Q

What is a typical zinc finger?

A

~23 amino acids with 2 cysteines and 2 histidines that chelate a zinc atom

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11
Q

How is the zinc finger domain formed?

A

by the interaction between the zinc atom with an alpha helix and an antiparallel beta sheet

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12
Q

What does each zinc finger recognise?

A

3 GC-rich nucleotides

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13
Q

What part of the zinc finger recognises the nucleotides?

A

amino acids 1, 2, 3 and 6

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14
Q

How can zinc fingers be artificially designed?

A

using ZFN (zinc finger nuclease) for genome editing

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15
Q

What is the homeodomain?

A

a conserved 60 amino acid domain particularly important during development

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16
Q

How is the homeodomain folded?

A

into 3 alpha helices (helices 2 and 3 are similar to the HTH motif)

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17
Q

What parts of the homeodomain contact the major and minor groove of DNA?

A
  • N-terminal arm lies in minor groove
  • helices 1 and 2 lie above the DNA
  • helix 3 lies in the major groove
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18
Q

What is the recognition sequence of homeodomain?

A

a core ATTA

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19
Q

What are the 2 binding domains that some homeodomain proteins contain?

A
  • POU domain that cooperates with the homeodomain to increase the binding specificity and affinity
  • paired domain binds to target DNA independent of the homeodomain
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20
Q

What is the bHLH?

A

a basic domain for DNA binding made up of 2 unequal helices

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21
Q

What allows flexibility of the bHLH?

A

a long loop which allows the helices to fold over each other and form a dimer through the HLH domain

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22
Q

What are bHLH proteins involved in?

A

cell differentiation in eukaryotes

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23
Q

What are the 3 bHLH proteins?

A
  • MyoD
  • E2A
  • Id
24
Q

What is MyoD?

A

a bHLH protein specifically expressed in muscle cells

25
Q

What is Id?

A

a bHLH protein without a basic region that forms a dimer with MyoD that inhibits formation of the MyoD-E2A dimer

26
Q

What is the E box?

A

the DNA binding motif for bHLH proteins; CACGTG

27
Q

What happens in the presence of Id?

A

the E box is not required and MyoD-E2A dimers do not form

28
Q

What is the frequency of leucine residues on the leucine zipper?

A

every 7 amino acids on only one side of the helix

29
Q

What is the leucine zipper?

A

an amphipathic helix; one face of the helix contains hydrophilic side chains and the other face contains hydrophobic side chains

30
Q

When does the leucine zipper protein function?

A

when it is a dimer

31
Q

What do Myc and Max contain?

A

both bHLH and Zip domains

32
Q

What do Myc and Max do?

A

form heterodimers by Zip domain interaction and bind to E box (CACGTG) of target genes

33
Q

What is Myc?

A

an important TF that regulates the transcription of ~15% of cellular genes

34
Q

What can overexpression of Myc cause?

A

cancer

35
Q

What can ADs interact with?

A

directly with GTFs or with cofactors

36
Q

What are the 4 types of activation domains?

A
  • acidic domains
  • gluatmine-rich domains
  • proline-rich domains
  • isoleucine-rich domains
37
Q

What is acidic/9aaTAD?

A

a loose consensus sequence essential for transcriptional activation

38
Q

What does acidic/9aaTAD interact with?

A

coactivators TAF9 and CBP/p300

39
Q

What is the acidic AD of CREB?

A

a bZIP TF

40
Q

How does the acidic AD of CREB work?

A

it folds into two amphipathic α-helices and interacts with co-activator CBP

41
Q

What are nuclear receptor TFs?

A

a group of zinc finger proteins that bind steroids in the cytoplasm and move into the nucleus where they bind the DNA and dimerise to activate transcription

42
Q

What does ligand binding to nuclear receptors cause?

A
  1. release of inhibitory proteins
  2. conformational change to seal the ligand
  3. binding of co-activator
  4. nuclear receptor binds to HRE to activate transcription by enhancing formation of transcription IC
43
Q

What does assembly of the multi-protein complex on HRE do?

A

enhance transcription by interaction with GTFs, TAFs and mediator protein

44
Q

What does every nuclear receptor have?

A

2 fingers; one for DNA binding and the other for dimerisation

45
Q

What do nuclear receptors bind to?

A

a short 15 nucleotide palindromic DNA sequence

46
Q

What are TGFs involved in?

A

a variety of activities in development, immune regulation, tissue repair, cancer

47
Q

What are the 4 steps of TGF-β signalling?

A
  1. extracellular ligand TGFβ binding results in tetramerisation of two receptors to phosphorylate intracellular domains
  2. activation of R-Smad
  3. formation of Smad trimers with C-Smad, common Smad4
  4. translocation to the nucleus and binding to responsive element to activate target genes
48
Q

What are the 5 steps of cAMP signalling?

A
  1. signal molecule binding to activate GPCR
  2. activated G protein and AC catalyse formation of cAMP
  3. PKA activation: cAMP binds to regulatory subunits to release catalytic subunits
  4. translocation to the nucleus to activate CREB by phosphorylating Ser-133
  5. binding to CRE and recruiting co-activator CBP activates target genes
49
Q

What is canonical Wnt signalling important for?

A

development and cancers

50
Q

What are the 5 steps of the canonical Wnt pathway?

A
  1. Wnt binds to Frazzled receptor
  2. Dishevelled and LRP are recruited
  3. inhibitory complex dissociates
  4. unphosphorylated β-catenin is released and translocates to the nucleus
  5. co-pressor Gruncho is displaced to activate target genes with TF LEF1/TCF
51
Q

What does TF dimerisation do?

A

increase DNA binding specificity and affinity as well as functional diversity

52
Q

What does each binding domain recognise?

A

4-6 nucleotides

53
Q

How can a single TF control several genes?

A

by interacting with different factors

54
Q

What does glucocorticoid receptor do?

A

co-ordinate expression of many different genes

55
Q

What does the effect of GR on GR-responsive genes depend on ?

A
  • presence of the GR
  • presence of the ligand
  • presence of other regulatory proteins
  • binding sites on the gene

Genes, Genomes and Biomedical Implications (15 decks)

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