Question

A. Answer Following questions.

1.A large number of class II promoters in the human genome lack TATA boxes. How does RNA Pol II recruitment differ between promoters with a TATA box and TATA-less promoters (2 pts)?

List 2 protein complexes that interact with the CTD of RNA Pol II during transcription

2. What class II gene(s) do not have a polyA tail (1pt)?

3.Polymerase recycling is an important mechanism for achieving high expression levels of a particular gene. What factors facilitate recycling (1pt), what regulatory step must occur (1 pt), why is this regulatory step important (1 pt)?

4.. Draw the 3’ Exon, Intron, and 5’ Exon after the first step of splicesomal intron splicing and before the second step. Be sure to show which components are connected (2 pts) and what the ends of the molecules look like- what are the functional groups at the ends (3pts).

5. If RNA Pol II incorporates the wrong nucleotide, what are the steps to relieve the pausing that results (3pts)?

6. Paused polymerases make excellent repressors. Describe which types of genes are likely to have paused polymerases- what is their expression profile (1pt). Why is a paused polymerase an excellent means to regulate these types of genes (3pts)?

7.List three functions of mediator in transcription (3 pts).

8. List two major findings from the ENCODE project (1pt).

9. Why do some people (not me) get upset if you call histone modifications “epigenetic marks” (2 pts)?

10. Where did Myc, Mad, and Max get their names? Besides the movie what do they stand for (2pts)?

Answer 1

1) The presence of a second group core promoter elements Inr, DPE, and MTE, which have been found in a both TATA-containing and TATA-less promoters, helps to explain transcription from some TATA-less genes.

TFIID recognizes and bind directly to Inr and DPE elements by using the TAF (TATA-binding protein [TBP]-associated factor) and leads to the formation of the pre-initiation complex on TATA-less genes.

For TATA containig genes, the TATA box bound by the TATA-binding protein (TBP) and other transcription factors ithat aid in formation of the pre-initiation complex.

Mediator, multiprotein complex that functions as a transcriptional coactivator and spliceosome factors intract with the CTD of RNApolII

2) Genes encoding for histones do not have a poly A tail

8) the first major discovery was that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another.

Another major discovery was that about half of functional elements in the human genome appear to have not been constrained during evolution. This was against the widely believed hypothesis that sequences important for biological function would be in areas of the genome most subject to evolutionary constraint

10)

Myc - MYC family of oncogenes

Mad - protein encided by Mxd 1 gene

MAX- Myc-associated factor X

Mad and MYC compete for binding to MAX and form a sequence-specific DNA-binding complexthat either acts as a transcriptional repressor? or activator.