Lecture 19 - Cis-Acting Regulatory Elements in RNA Polymerase II Promoters Flashcards
In mammalian cells, where does the TATA box usually sit?
Somewhere Between -26 and -31
What does the initiator element (Inr) do?
The initiator element plays some role in appropriately positioning and enhancing the efficiency of initation, but it’s not as important as TATA.
Where is the initator element (Inr) usually found?
It is usually situated around the transcription start site, where usually there is a C at the -1 site and an A at the +1 site.
What is the TFIIB recognition element (BRE)?
The BRE is the site where TFIIB interacts with the DNA.
What do the downstream promoter elements (DPE) do?
The DPEs contribute to transcriptional efficiency.
How much of the genome is transcribed?
80%
With promoters that work in both directions, what kind of transcripts can be formed?
Sense transcripts are formed, but very often, antisense transcripts can also be formed.
Where are divergent transcripts usually prevalent?
Divergent transcripts are usually prevalent on promoters that have CpG (C phosphate G) islands and those that do not have TATA boxes.
What is divergent transcription?
Divergent transcription is when both sense and antisense transcripts are produced by reading on both sides of the promoter.
Why do CpG regions give rise to divergent transcription?
CpG regions can be read from either side of the double stranded DNA, so polymerase will join on both sides.
Which type of transcript is made more in divergent transcription? Why might this be?
Sense
This may be because of the presence of splicing sites in the antisense direction, which may give rise to an elongation problem, or disrupt transcript stability.
What are promoter-proximal elements? What do they do?
Promoter-proximal elements are other conserved sequences that are important for the activation of specific genes. They may be recognized by specific proteins that interact with DNA and enhance transcriptional efficiency of the downstream genes.
Where are enhancers found?
Enhancers tend to work distally in promoters, far from the transcription start sitres. They can be kilobases upstream or downstream of the gene that they are affecting.
What is the difference in directionality between promoter-proximal elements and enhancers?
Enhancers work in a non-directional way. You can flip them around and they are equally effective. This is not the case for promoter-proximal regions.
What do yeasts have instead of enhancers? Why?
Yeast genes have very few introns and the TATA boxi s present around -90 (quite far from the transcription start site). Instead of having enhacers, they have upstream activating sequences (UAS), which are upstream of the TATA box in these gemes but often not as far away as the enhancers in mammalian genes.
What does mammalian genes having distant regulatory elements suggest?
Mammalian genes having distant regulatory elements suggests that they are involved in setting up topological domains in the chromatin, which brings them in proximity to the given promoters of the gene that they are affecting.
What does the PAX6 gene in humans play a role in?
Development of the Eyes
What do enhancers very often respond to?
Enhancers very often respond to DNA-binding proteins that are specific to given tissues. These are called tissue/temporal-specific DNA-binding transcription factors.
How can you use recombinant DNA technology to analyze what the proximal region does to transcriptional output?
You can use recombinant DNA technology in order to make plasmids that have a series of deletions that you can generate in a 5’ to 3’ manner, where you whittle down the proximal region of a given control region of a gene, then analyze what the pertubations in that proximal region do to the transcriptional output of that target gene (via looking at a reporter gene). In order to get the plasmids into mammalian cells, they are amplified in bacteria and then transfected into mammals.
What are transformation, transfection, and transgenics?
Transformation involves the insertion of DNA into a specific vector that can grow in bacteria. It allows DNA amplification and purification. Transfection and transgenics involve the introduction of similar vectors into mammalian cells and into animals or plants (respectively).
How can you whittle down the proximal region of a given gene?
You can make increasingly smaller, overlapping PCR constructs of the proximal region.
What are reporter genes?
Reporter genes are genes that allow you to assess gene expression.
GFP, β-galactosidase, thymidine kinase, chloramphenicol, and luciferase are all examples of what?
Reporter Genes
Which regions of the genome do and don’t have variation between organisms?
There’s a large amount of variation between organisms in the nucleotide sequences of the regions that don’t necessarily have important consequences downstream. In regions where any change will increase change of death, there’s very clear selection against changes in those regions.
