Biostar Beta. Not for public use.
Question: Choosing a best possible TES based upon H3K36me3 or other ChIP data
0
Entering edit mode

I was wondering if any researchers have a method to choose a best TES of a gene using K36 or some sort of NGS data to use in a coverage plot. We have chosen the best TSS using pol2 data but we are trying to experiment with ways to choose TES and are wondering if any other bioinformaticists have a way they choose.

ADD COMMENTlink 4.6 years ago ac • 20
Entering edit mode
0

Could you clarify TES? You say TSS at one point but TES in other locations, including the title.

ADD REPLYlink 4.6 years ago
SES
8.2k
Entering edit mode
0

Best to avoid too much jargon, or at least define it up front. TES = Transcription End Site (as opposed to TSS, Transcription Start Site), and sometimes referred to as TTS = Transcription Termination Site. K36 = H3K36me3, pol2 = RNA pol II. Also, "best" is a hairy term, dependent on the question you're asking (which isn't specified in the question above). "Best" is defined relative to some purpose. For TSS, if a gene has many choices of TSS, you chose the "best" one by taking the one with the highest pol II signal, as presumably this would indicate which TSS is being used by the locus, but this could depend on which pol II antibody was used for polymerase detection. For TES, if many choices are available, "best" might be defined as H3K36me3 signal 5' of TES, but less signal 3' of TES. Your question might be rephrased: is there a chromatin mark or signature that defines Transcription Termination Sites? Or does anyone have a method for correlating or scoring Transcription Termination Sites with active marks of transcription, such as H3K36me3?

ADD REPLYlink 4.6 years ago
seidel
6.8k
This thread is not open. No new answers may be added
Similar Posts
Loading Similar Posts
Powered by the version 2.0