The chip-seq binding sites of POLR2B indicate the PoII pause there

Question

[limeng]

I noticed chip-seq for POLR2B which is a core component of PoII, have a lot of binding sites in gene body? Is this because the PoII pause there? or since PoII is rapidly moving, why it have binding sites?

Answer 1

[Carlo Yague]

One possible explanation: Pol II pauses on introns.

Answer 2

[Prakash]

During transcription, pol II elongates over gene body. When you perform ChIPseq, you will find pol II density over promoter as well as gene body. The ratio of pol II enrichment at promoter and gene body determines whether gene is transcribed or not.