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Gene Regulation and Expression > Transcription and Splicing > Flashcards

Transcription and Splicing Flashcards

1
Q

First step of gene expression

A

transcription = taking DNA and making it into RNA

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2
Q

What enzyme is responsible for transcribing genes

A

RNA Polymerase at the active site

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3
Q

Mechanism of RNA Polymerase

A
  • separates two DNA strands in a transient bubble (12-14 bp, length of RNA-DNA hybrid within it is ~8-9 bp)
  • uses one strand running 3’-5’ as a template to direct synthesis of a complementary sequence of RNA running 5’-3’
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4
Q

What are the three domains of life

A

Bacterial, Archaeal and Eukaryotic

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5
Q

What is meant by the statement “Transcription in eukaryotes is pervasive”

A
  • genome is being transcribed abundantly
  • a substantial portion of non-coding DNA sequences with important biological functions are transcribed into RNA molecules
  • 12% of genes are transcription factors that regulate gene expression and transcribe themselves (chicken and egg)
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6
Q

What initiates transcription in eukaryotes

A

many proteins and complex cis-regulatory elements

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7
Q

What genes does RNA Polymerase I transcribe

A

5.8S, 18S, 28S rRNA genes

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8
Q

What genes does RNA Polymerase II transcribe

A

all protein-coding genes, plus snoRNA genes, miRNA genes, siRNA genes, IncRNA genes, and most snRNA genes

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9
Q

What genes does RNA Polymerase III transcribe

A

tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs

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10
Q

Why does RNA Polymerase II require a set of general transcription factors

A

RNA Polymerase II binds non-specifically and cannot recognize a gene promoter, so needs to be actively recruited to initiate transcription

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11
Q

Which transcription factor recognises the promoter

A

TF2B -> able to recruit RNA Polymerase in conjunction with TF2F

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12
Q

Role of core promoter sequence

A
  • defines where transcription begins
  • interact with RNAP II GTFs
  • basal levels of transcription initiation
  • located immediately upstream (5’) of the transcription start site
  • fixed direction/orientation relative to gene
  • unsymmetrical
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13
Q

TF2D composition

A

TBP and ~11 additional subunits called TAFs; C-terminal domain

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14
Q

Rold of TBP subunit (1)

A

recognises TATA box

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15
Q

Role of TAF subunits (~11)

A
  • recognise BRE element in promoters
  • recognise other DNA sequences near the transcription start point
  • regulates DNA-binding by TBP
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16
Q

Role of TF2B subunit (1)

A
  • recognises BRE element in promoters
  • accurately positions RNA polymerase at start site of transcription
17
Q

Role of TF2B subunits (3)

A
  • stabilises RNA polymerase interaction with TBP and TFIIB
  • helps attract TFIIE and TFIIH
18
Q

Role of TFIIE subunit (2)

A
  • attracts and regulates TFIIH
  • stabilises open complex and allows for RNA synthesis
19
Q

Role of TFIIH subunits (9)

A
  • unwinds DNA at transcription start site
  • phosphorylates Ser5 of the RNA polymerase CTD
  • releases DNA polymerase from promoter
20
Q

What is mRNA processing

A

capping, splicing, and 3’ end formation are associated with CTD of Pol II

21
Q

What is DNA damage repair

A

DNA helicase subunits of TF2H have a role in nucleotide excision repair; transcription-coupled repair

22
Q

Nuclear architecture

A

nuclear matrix, chromosomal domains; transcription foci in the nucleus; eu- vs. heterochromatin

23
Q

DNA replication

A

transcription factor binding sites near origins of replication; actively transcribed genes are replicated in early S phase

24
Q

How are S values related to rRNA name

A
  • S value refers to rate of sedimentation in an ultracentrifuge
  • larger S value = larger rRNA
25
Q

Role of enhancers and silencers

A
  • modulate (up or down) levels of initiation at the promoter
  • orientation independent
  • location variable/flexible: kilobases away from the promoter; up- or downstream of gene
  • binding sites for multiple transcription factors (transcriptional activators)
26
Q

What are ‘transcriptional activators’

A
  • molecular proteins with multiple distinct domains
  • DNA-binding domain: bring transcription-activation into the vicinity of promoter
  • Activation domain: transcriptional activation
  • Dimerisation domain: cooperativity in DNA binding
27
Q

Sequence can be recognised and bound by transcription factors through which point

A

DNA binding domain

28
Q

Transcription factor dimerisation

A

by combination of different activators or repressers you can recognise lots of different sequences within a genome
- in homodimerisation, binding domain evolves to recognise palindromic sequences

29
Q

What happens if a gene heterodimerises with an inhibitory factor

A

gene regulated through site is not recognised as it is inhibited

30
Q

What is an enhanceosome

A
  • multitude of transcription factors assembling into a macromolecular complex at enhancer sequences
  • transcription activators work synergistically
  • enhancers work from distance to modulate the assembly of the transcription machinery at promoter
31
Q

Role of insulators

A

prevent eukaryotic transcription regulators from influencing distant genes; long-range control

32
Q

Who are chromosomal domains defined

A

by matrix attachment regions

33
Q

How does an activator activate transcription

A
  • promote the assembly of a transcription pre-initiation complex (recruitment of GTFs and RNA Pol II) at the start site of transcription
  • direct modification of local chromatin structure through recruitment of chromatin remodeling activities
  • releasing RNA Polymerase from promoters or pause sites
34
Q

Describe the method of chromatin remodeling activites

A

-

35
Q

Evidence for chromatin remodeling activites directing the modification of local chromatin structure

A
  • fluorophore marker
  • induction of an activator expression results in large-scale chromatin unfolding (decondensation) through recruitment of remodeling complexes

Gene Regulation and Expression (10 decks)

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