W4 Transcriptional circuits Flashcards
Transcriptome
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
Housekeeping genes
Genes that code for proteins required for all cell types (e.g. glycolytic enzymes)
Tissue-specific
Only in certain cells of certain tissue for e.g. globin in RBC
Inducible genes
Genes transcribed in response to stumili (infections etc). Code for proteins required to respond to the stimuli
Transcription requires recognition sequences in DNA
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’)
Enhancers
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”
Enhancers dependent
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
Recruitment of RNA polymerase to promoters
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
PK promoters
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
Consensus sequence
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
Regulatory transcription factors
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
Transcriptional switches
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)
Lac ZYA
Genes needed to utilise lactose as a carbon source (code for enzymes that hydrolyse lactose for energy)
One gene that codes for 3 proteins
CAP (Catabolite activator protein)
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
Lac repressor
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)
Regulatory transcription factors process
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
Some common regulatory elements
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
Steriod hormone signalling
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
Tamoxifen
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
GATA 1
TF only expressed in RBC
Binds to promoter + enhancer regions
Restriction point in cell cycle
All enzymes for DNA (synthesis) replication are present
Insensitive to external environment
Cell cycle transition
G1-S transition requires transcriptional activation of genes that encode proteins involved in DNA replication
Cdks target TFs
E2F
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)
pRB repression
Mitogenic stimulus Induce Cdk Phosphorylate pRB Change in shape Can't bind E2F So E2F can recognise ... etc
Retinoblastoma exploited by viruses
Exploited by viruses to cause cancer
Viral oncogene competes w/E2F for binding to RB
So allows virus to promote + control cell growth
Retinoblastoma w/loss of one gene
Cancers of retina
Lose one copy og RB
Can not suppress S phase
Cells replicate uncontrollably by mitosis
