6th Feb - TFs 1 Flashcards

1
Q

What are transcription factors?

A

Adaptor molecules that detect regulatory sequences in the DNA and target the assembly of protein complexes that control gene expression

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2
Q

How were enhancers originally identified?

A

As SV40 DNA elements that could upregulate host beta-globin gene expression

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3
Q

What are enhancers?

A

DNA elements that activate gene expression from a distance, irrespective of their orientation

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4
Q

Roughly how many active enhancers are present per cell?

A

10000-15000

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5
Q

What is 3C?

A

Chromosome conformation capture

  1. Cells are crosslinked with formaldehyde to link chromatin segments that are in close spatial proximity
  2. Chromatin is fragmented by restriction digestion or sonication
  3. Crosslinked fragments are ligated to form unique hybrid DNA molecules
  4. DNA is purified and analysed
    - –This is where the variation of methods occurs
    - –Traditional uses individual PCR to detect single ligation products one at a time
    - –4C uses inverse PCR to generate genome wide interaction profiles for single loci
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6
Q

How were enhancers and their local interactions identified across the genome?

A

Using 3C

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7
Q

What histone modifications are common at inactive enhancers?

A

H3K27me3

H3K4me1

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8
Q

What histone modiciations are common at active enhancers?

A

H3K4me1

H3K27ac

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9
Q

What are pioneer TFs?

A

(master TFs)

Bind independently of nucleosomes, preceeding other factors binding

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10
Q

What are super enhancers?

A

Multiple enhancers in close proximity combined, they determine cell fate

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11
Q

What are hotspots?

A

Large nucleosome free regions to which multiple factors bind

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12
Q

How were enhancer RNAs discovered?

A

Through GRO-seq

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13
Q

What are the three models of eRNA function?

A
  • Noise from unspecific recruitment of PolII i.e. PolII binds on any open DNA soon realises its in the wrong place and terminates transcription
  • Mechanism of enhancer function - released from the transcribed enhancer and somehow communicates with the promoter
  • eRNAs play an important functional role
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14
Q

What is specificity?

A

The difference in Kd between one site and another

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15
Q

What are the different ways TFs have evolved to overcome transient DNA binding and lack of specificity?

A

Variable spacing - half sites seperated by variable length spacers

Multiple DBDs - e.g. Oct1 can bind to different DNA sites using different arrangments of its 2 DBD motifs

Multi-meric binding - Elk1 can bind as either a monomer or dimer

Alternative structural conformations - SREBP can bind to different DNA sites by adapting alternate structural conformations

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16
Q

What percentage of genes encode TFs?

A

About 6-7%

17
Q

How is co-operative binding utilized by TFs?

A

Gives enhanced complex stability due to co-operativity which allows binding to lower affinity aites
OR
Inter protein interactions alter protein DNA contacts, altering DNA binding specificity

18
Q

What is the stucture of the Mad-max DNA binding motif?

A

Helix-loop-helix

19
Q

Why do zinc fingers contain zinc?

A

It holds the structure together, as disulphide bonds can’t be maintained in the reducing atmosphere of the nucleus