Research article.
With reference to the research article from Nojima et al., Cell 2015 [1], discuss the relevant data and write a series of paragraphs addressing the following points:
a. Briefly describe the mNET-seq technique and explain two advantages and two disadvantages compared to
i) RNA Pol II ChIP-seq method and ii) PRO-seq assays. (30%)
b. Describe where and how the termination of Polymerase II takes place across the genome at the molecular level. Explain the biological significance of the regulation of transcription termination in regard to gene expression. (40%)
c. With reference to the paper, explain how Polymerase pausing proximally to promoters and at the transcription termination site (TES) are linked to mechanisms of transcription termination. What was the phosphorylation status of the CTD of Pol II molecules found by the authors to be associated with promoter-proximal pausing, splicing sites and the TES? How, in your opinion, can differential phosphorylation of the CTD dictate and control the different co-transcriptional activities of transcriptional termination and splicing that take place across the gene? (30%)
Reference: Nojima, T. et al. Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell 161, 526-540, doi:10.1016/j.cell.2015.03.027 (2015).