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GENE3340 MOLECULAR GENETICS > Gene regulation > Flashcards

Gene regulation Flashcards

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1
Q

What are the levels of control of gene expression?

A
  • transcription
  • RNA processing
  • Transcriptional regulation
  • post-transcriptional regulation
  • epigenetic
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2
Q

Transcription produces 3 main types of RNA, what are they?

A
  • rRNA, mRNA, tRNA (also many small RNAs)
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3
Q

What does the typical eukaryotic promoter refer to?

A
  • usually refers to the whole 5’ region including the promoter proximal elements and upstream enhancer elements
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4
Q

What can be used to initiate transcription in eukaryotes?

A
  • TATA box and Initiator sequence (inr)
  • TATA box is used in genes that are rapidly transcribed. Less than 50% of all genes have a TATA box. ~ -35 to -25 (consensus sequence)
  • Initiator sequence used when genes don’t have a TATA box. Exact sequence determines strength of initiator. Initiator sequence begins at a defined site +1 (an A)
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5
Q

Other than TATA or initiation sequence, what are the other RNA pol II core promoter elements?

A

BRE - TFIIB recognition element (GC rich)

DPE - Downstream core promoter element

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6
Q

What are the complex of proteins that bind to either TATA or initiation sequence in transcription?

A
  • Called TFs
  • Designated TFIIA, TFIIB etc - most are multimeric proteins
  • Large (composed of TATA box binding protein TBP and TBP associated factors (TAFs)
  • TAFs are involved in RNA pol positioning in non TATA containing genes
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7
Q

What are the steps initiation of transcription?

A
  1. TFIID binds to TATA box via the TBP subunit and bends DNA
  2. TFIBB binds and makes contact with both TBP and the DNA
  3. A complex of TFIIF and Pol II binds such that the Pol II is positioned over the start site
  4. TFIIE binds and forms a docking site for TFIIH
  5. TFIIH binds to 2 subunits that have helicase activity
  6. TFIIH unwinds the DNA (requires ATP) at the start site (allows release of general TFs, allows pol to move down DNA and synthesise RNA
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8
Q

What are 2 of the sequence specific TF binding elements?

A
  • Promoter-proximal elements occur near the start site - position dependent
  • enhancer elements can occur far upstream, in introns or downstream of the genes in higher eukaryotes - position independent
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9
Q

What are the distance-independent promoter elements?

A
  • enhancers are cis-elements (DNA) that bind TFs and increase transcription rates
  • silencers are cis-elements that bind silencer proteins and decrease transcription rates
  • enhancers and silencers are similar to proximal-promoter elements except they act as a distance by DNA looping (facilitated by architectural proteins)
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10
Q

What are transcription factors?

A

A TF is a sequence specific DNA binding protein that recognises a short DNA sequence.

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11
Q

What common protein motifs physically interact with specific DNA sequences?

A
  • zinc fingers

- leucine zippers

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12
Q

What is combinatorial control?

A
  • cooperative interactions between cis elements
  • enable fine tuning of transcriptional control
  • having multiple cis elements in right arrangement can lead to amplified response (synergistic effect)
  • leads to the formation of an Enhanceosome
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13
Q

What is the enhanceosome?

A

A large transcription factor complex that acts synergistically

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14
Q

What is chromatin’s role in gene regulation?

A
  • highly condensed heterochromatin has a general silencing effect
  • open euchromatin is transcriptionally more active
  • chromatin also acts locally to directly control transcription
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15
Q

What is chromatin composed of?

A

DNA and histones (plus other chromosomal proteins)

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16
Q

What does the nucleosome contain?

A

Histones; H2A, H2B, H3 and H4

- histone H1 binds between and keeps the nucleosome intact

17
Q

How can modifications of histone tails control chromatin condensation and function?

A
  • each histone has a flexible N-terminus extending out from the nucleosome
  • H2A and H2B also have flexible C-term tails
  • histone tails subject to modification
18
Q

What’s the histone code?

A

Only a subset of modifications present on any histone. Histone marks = epigenetic regulation

19
Q

Do histones from heterochromatin contain different marks than histones from euchromatin?

A
  • YES
  • lysine residues are often acetylated in extended conformations
  • acetylation neutralizes the +ve charge of lysine important in maintaining the 30nm fibre
  • methylation prevents acetylation
20
Q

What reads the histone code?

A
  • read by proteins with a chromodomain (e.g. HP1 - heterochromatin protein 1)
  • HP1 chromodomain binds to tri-methylated H3K9
  • HP1 chromoshadow domain interacts with other proteins with the same domain - oligomerization of HP1
  • result is condensation of chromatin (heterochromatin)
  • HP1 chromoshadow domain also interacts with domain of H3K9 histone methyltransferase
  • leads to tri-methylation of adjacent H3K9s -spreading of heterochromatin (chain reaction)
  • boundary elements prevent condensation spreading to active chromosome regions
21
Q

What can gene transcription be activated by?

A

Histone acetylation

22
Q

How do transcriptional activators regulate assembly of the initiation complex?

A
  • TF bind cognate sequence
  • TF contacts Mediator complex
  • very large complex (30 subunits)
  • molecular bridge to initiation complex
23
Q

What does the highly ordered multistep process of transcription involve?

A
  • sequence-specific TFs
  • chromatin remodelling complexes
  • histone acetylation complexes
  • a mediator complex
  • general TFs
  • RNA pol
24
Q

Describe the steps of transcription in a yeast HO gene

A
  1. Gene decondensed by SWI5 binding at enhancer site upstream of gene and interacting with SWI/SNF
  2. SWI/SNF remodels chromatin exposing tails
  3. GCN5 recruited by SWI5 and acetylates histone tails. SWI/SNF continues de-condensation
  4. SWI5 released but SWI/SNF and GCN5 remains associated by binding acetylated histone tails. Remodelling allows binding of TF SBF to exposed DNA
  5. Mediator complex binds transcriptional activator SBF
  6. Preinitiation complex is formed via interaction with mediator complex
25
Q

What is a super enhancer?

A

Formed by exceptional amounts of TFs and control the expression of gene critical for cell identity

26
Q

What are the types of levels of controls of RNA splicing?

A
  • some ubiquitous others tissue-specific
27
Q

What are the 3 sequences needed for splicing?

A
  1. Splice donor including invariant GU at 5’ end on intron
  2. Splice acceptor including invariant AG at 3’ end on intron
  3. Branch site near splice acceptor (invariant A) initiates splicing reaction
28
Q

What sequences regulate RNA splicing?

A
  • enhancers and suppressors that are introns (ISS, ISE) or exons (ESE,ESS)
  • can produce different proteins
29
Q

What percentage of genes are alternatively spliced?

A
  • 90% in humans
30
Q

What is an example of alternative splicing leading to 2 different proteins?

A

CDKN2A gene leads to 2 different tumour suppressor proteins:

  1. P14ARF
  2. P16INK4A
    - different reading frames due to alternative promoter usage and splicing
31
Q

What is translational regulation?

A

Mechanism to allow rapid response to environment. Mediated via RNA-secondary structures and RNA-binding proteins

32
Q

What’s an example of translational regulation?

A

Iron metabolism - ferritin and transferrin receptor

- IRE (iron-responsive element) in mRNA binds to IRE-binding protein (IRE-BP) when FE concentration low

33
Q

In Iron metabolism what happens when FE concentration is low in the different IRE locations?

A
  • in 5’IRE in ferritin mRNA block translation

- in 3’ IRE in transferrin-R stabilizes mRNA

34
Q

What is a microRNA?

A

A small RNA molecule that forms after transcription, through a series of cleavage and processing steps. MiRNAs bind to mRNAs and regulate their activity level. An example of post-transcriptional gene silencing. A single miRNA can regulate multiple mRNAs

35
Q

What are Long noncoding RNAs?

A

Non-protein en-coding transcripts longer than 200bp. Account for 4/5 of transcription. Participate in chromatin organisation and transcriptional and post-transcriptional gene expression. Also act as structural scaffolds of nuclear domains

36
Q

What resembles mRNAs?

A

Long noncoding RNAs (5’ capping, splicing, polyA)

GENE3340 MOLECULAR GENETICS (20 decks)

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