Transcriptional circuits Flashcards
What is the transcriptome?
Most of the eukaryotic genome is never transcribed
The segment that is transcribed is referred to as the transcriptome
Only a fraction of the transcriptome is transcribed at any one time
What are the different levels that genes can be transcribed to?
Abundant, rare or no transcript
If a gene is on in every gene this is called a housekeeping gene (e.g. glycolytic enzymes)
Tissue-specific genes are are of no transcript in some tissues and abundant in others e.g. globin
Inducible genes go from rare or no transcript to abundant transcript by activation through a stimulus
What are 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 in an intron
Like promoters, enhancers contain DNA sequences that are very strong binding sites for specificity factors or ‘transcription factors’
How is RNA polymerase recruited to promoters?
Neither prokaryotic nor eukaryotic RNA polymerases make stable contacts with DNA- they slide along the duplex without being able to efficiently recognise promoters
Recognition of promoters is mediated by initiation factors
Predominantly sigma factor for prokaryotes
The TFII basal transcriptional machinery for eukaryotes
Once stably recruited to DNA, RNA polymerase is able to convert from a closed to an open complex
How do sigma factors mediate recognition of promoters?
Sigma factor recognises the -35 and -10 motifs common to prokaryotic promoters and enables RNA polymerase to make stable contacts with DNA
The - refers to the bases away from the initiation site
What is a consensus sequence?
A consensus sequence is the sequence you are likely to find if you were working on a new promoter
What are regulatory transcription factors?
The ability of sigma factors and TFII to recruit RNA polymerases to promoters are generic
This does not account for the ability to vary the level of transition from a promoter
In both prokaryotes and eukaryotes they function to dramatically alter the level of recruitment of RNA polymerase and/or its ability its ability to initiate transcription
Additionally, in eukaryotes they can influence local chromatin structure
How do regulatory transcription factors function?
Regulatory transcription factors recognise and bind specific DNA target sequences
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
What are some examples of transcriptional switches in prokaryotes and eukaryotes?
Prokaryotic:
The lac operon
Eukaryotic:
Oestrogen-responsive transcription
Tissue-specific transcription (beta-globin)
A complex regulatory circuit (cell cycle)
What is the lac operon?
A prokaryotic paradigm for the regulation of transcription
How is the transcription controlled in bacteria using the lac operon?
With both glucose and lactose the operon is off because CAP protein is not bound (Only active under low glucose conc.)
With glucose but not lactose the operon is off both because the lac repressor is bound to the DNA and because CAP is not bound
With neither glucose not lactose the operon is off because the lac repressor is bound
With no glucose but lactose is present the operon is on because CAP is bound and lac repressor is unbound from lactose binding to repressor
How does steroid hormone signalling work with oestrogen?
Oestrogen is a steroid hormone- lipophilic so can cross membrane easily
It binds to the oestrogen receptor which leads to a conformational change meaning it van traverse the cell nucleus and scans and binds to its specific DNA sequence which will recruit efficient RNA polymerase II so you can transcribe RNAs that are specific for the response
What is Tamoxifen?
A therapeutic drug that works by interfering with interactions between regulatory and general transcription factors
This can block the cell division of breast cells thereby decreasing the chance of dividing breast cancer cells
Describe how tissue-specific transcription with beta-globin as an example?
Beta-globin is only expressed in red blood cells or cells that eventually turn to red blood cells
As red blood cells differentiate, NF, CP1 and Sp1 are ubiquitous factors- they start producing the expression of this gene
But ultimately the important transcription factor is GATA-1
GATA-1 is a tissue-specific factor so only expressed in differentiated red blood cells
Therefore GATA-1 will bind ton the promoter region which will recruit RNA Pol II efficiently and promote the expression of beta-globin in only red blood cells
How is EF2 activity repressed in G0 and early G1 by the product of the Retinoblastoma gene (pRB)?
pRBs bind to the EF2 factors to inhibit them
If you have a mitogenic stimulus, then you get the activation of cyclin and cyclin-dependant kinases which results in the phosphorylation of pRBs which changes their shape to the point where they can no longer bind to the EF2 transcription factors
