The Impact Of Adenine-Rich Tracts On Pol Ii Pausing

Question

[polarise]

Hi Biostars,

I'm studying alternative splicing in the context of cotranscriptional splicing. I've found a paper (Saeki & Svejstrup 2009, Sigurdsson et al. 2010, Close et al. 2012) that mentions that A-rich tracts cause pausing. The first paper does not provide a reference on this but all the other cite it and each other.

Is pol II pausing by A-rich tracts common knowledge or can anyone point me to some references?

Thanks PK

Answer 1

[Allpowerde]

You could download publicly available RNAseq (whole RNA rather than Poly-A-tail filtered is more appropriate) data and have a look at the coverage at the transition from an A-rich region to regions with "normal" bp distribution. If there is pausing then I would expect more actively transcribed transcripts to end at A-rich regions hence the coverage should drop noticeable after A-rich areas.