W4 Transcriptional circuits Flashcards

1
Q

Transcriptome

A

Segment that is transcribed

Only a fraction of the transcriptome is transcribed at any one time

Most of EK genome is never transcribed (10000/50000 expressed)

50% of PK genome is transcribed

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2
Q

Housekeeping genes

A

Genes that code for proteins required for all cell types (e.g. glycolytic enzymes)

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3
Q

Tissue-specific

A

Only in certain cells of certain tissue for e.g. globin in RBC

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4
Q

Inducible genes

A

Genes transcribed in response to stumili (infections etc). Code for proteins required to respond to the stimuli

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5
Q

Transcription requires recognition sequences in DNA

A

The sequence immediately 5’ to the region to be transcribed is called a “promoter”
Promoters recruit RNA polymerase II to a DNA template
RNA polymerase can only move one way (5’ to 3’)

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6
Q

Enhancers

A

Sequences of DNA that are not immediately adjacent to where transcription starts that act to enhance the recruitment of RNA polymerase to a promoter
Enhancers can reside 5’ or 3’ to a transcription unit, and can even be located within an intron
Like promoters enhancers contain DNA sequences that are very strong binding sites for specificity factors or “transcription factors”

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7
Q

Enhancers dependent

A

Orientation independent = can cut out DNA and place it the other way and can still work
Both upstream/downstream
Distant from transcription site
Position independant

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8
Q

Recruitment of RNA polymerase to promoters

A

Neither PK/EK RNA polymerases make stable contacts with DNA = slide along duplex without being able to efficiently recognise promoters

Recognition mediated by initiation factors:
PK = (predominantly) sigma factor which binds to promoter
EK = TFII basal transcriptional machinery (TFIID + TBP needed as recognition site for TATA box)

Once stably recruited to DNA, RNA polymerase is able to convert from a closed to an open complex

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9
Q

PK promoters

A

Sigma factor recognises the -35 and -10 motifs common to prokaryotic promoters
and enables RNA polymerase to make stable contacts with DNA.
Also binds to TATA

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10
Q

Consensus sequence

A

Align promoters + most abundant sequence. Most likely sequence which is highly represented will be the CS.
If not present doesn’t mean that sigma binding site not present on promoter

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11
Q

Regulatory transcription factors

A
The ability of sigma factor and TFII to recruit RNA polymerases to promoters are GENERIC – i.e. they happen at every promoter 
This does not account for the ability to VARY the level of transcription from a promoter
Regulatory changes are mediated by a different class of transcription factors = Regulatory Transcription Factors 
In both prokaryotes and eukaryotes they function to dramatically alter the level of recruitment of RNA polymerase and/or its ability to initiate transcription
Additionally, in eukaryotes they can influence local chromatin structure
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12
Q

Transcriptional switches

A

PK:
The lac operon (a prokaryotic paradigm for the regulation of transcription)

EK:
Oestrogen-responsive transcription
Tissue-specific transcription (beta-globin)
A complex regulatory circuit (cell cycle)

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13
Q

Lac ZYA

A

Genes needed to utilise lactose as a carbon source (code for enzymes that hydrolyse lactose for energy)
One gene that codes for 3 proteins

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14
Q

CAP (Catabolite activator protein)

A

Only active under low [glucose]
CAP binds to promoter + recruits RNA PII and induces expression of gene (Lac ZYA)

RNA PII only recruited if CAP protein bound to promoter

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15
Q

Lac repressor

A

If [glucose] + [lactose] high then no need to express Laz ZYA
Lac repressor binds to promoter so gene not copied
Will use lactose when [glucose] levels low
Lactose binds to repressor
Repressor can’t bind to promoter
RNA PII recruited (due to change of shape)

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16
Q

Regulatory transcription factors process

A

Regulatory factors recognise their target sequences by interacting (binding) w/DNA

They do not have to unwind the DNA double helix to see their target
Therefore an intact DNA molecule can present information to the cell

17
Q

Some common regulatory elements

A

Trigger: Immune stress
Regulatory element: GGGANNNTCC
Transcription factor: NF-kB

Trigger: Cyclic AMP
Regulatory element: TGACGTCA
Transcription factor: CREB

Trigger: Oestrogen
Regulatory element: GGTCANNNTGACC
Transcription factor: Oestrogen receptor

Trigger: Interferon (produced in cells infected by viruses)
Regulatory element: GAAANNGAAACTG
Transcription factor: ISGF3

Genes only expressed when these TFs (which recognise sequences) binds to RE so can recruit RNA PII

18
Q

Steriod hormone signalling

A

Steriod hormone crosses CM
Oestrogen binds to Oestrogen receptor causing change in shape
O-OR complex scans for oestrogen responsive sequences + binds
Facilitate recruitment of TFIID
Thus recruitment of RNA PII
Gene transcribed
RNA translated into protein

Oestrogen receptor usually in cytoplasm + translocates when receives oestrogen

19
Q

Tamoxifen

A

Was used in breast cancer (not now = side effects)
Antagonist of oestrogen-responsive transcription
Competes w/oestrogen to bind to receptor (reversible)
Breast cancer cells need oestrogen for survival (cell growth)
Unable to recruit RNA PII
Oestrogen responsive genes shutdown

20
Q

GATA 1

A

TF only expressed in RBC

Binds to promoter + enhancer regions

21
Q

Restriction point in cell cycle

A

All enzymes for DNA (synthesis) replication are present

Insensitive to external environment

22
Q

Cell cycle transition

A

G1-S transition requires transcriptional activation of genes that encode proteins involved in DNA replication
Cdks target TFs

23
Q

E2F

A

Promoter for G1-S transition genes
Recognise specific DNA sequences (E2F sites) to promote S phase

E2F activity repressed in G0 and early G1 by the product of the retinoblastoma gene (pRB)

24
Q

pRB repression

A
Mitogenic stimulus
Induce Cdk
Phosphorylate pRB
Change in shape
Can't bind E2F 
So E2F can recognise ... etc
25
Q

Retinoblastoma exploited by viruses

A

Exploited by viruses to cause cancer
Viral oncogene competes w/E2F for binding to RB
So allows virus to promote + control cell growth

26
Q

Retinoblastoma w/loss of one gene

A

Cancers of retina
Lose one copy og RB
Can not suppress S phase
Cells replicate uncontrollably by mitosis