ChiP-seq and RNA-seq

[TheSeqGeek]

I was wondering if anyone has done both ChIP-seq and RNA-seqand observed that while you have a DNA binding site inside the gene or on the promoter region of a gene, but the gene expression did not change according to RNA-seq.

Ruling out bad data what other explanations would reconcile this?

[dpryan]

There's lots of non-functional protein binding to DNA, just see almost any critique of the ENCODE papers for examples.

[Julian_R]

Hi,

I would like to connect transcription factors binding sites with RNA data.
As a approximation I would like to take promoters and other things such as gene bodies, introns e.t.s. and map localization of TF for set of gens expressed in mt samples.
I was surprised to find that cufflinks output does not contain strand information.
Without it it's difficult to interpret the data. Interestingly, in the merged GTF file they do, but in final files with expression data - they don't. So, how to glue one to another given that they have unique ID ?

Any advice would be appreciated.


Thank you.

[dpryan]

If I recall correctly, cufflinks/cuffmerge will only contain strand information if you use (and tell it/them that you used) a stranded library. If not, it has no way to determine strand.

[Julian_R]

no strands in cufflnks

Thank you for you reply.

Yes, of course It is stranded.
I have strand informatin in the merged GTF file.
I do not have strands in the resulted file that contains ratios.
I will double check if number of entities is the same in merged GTF and results.

[TheSeqGeek]

There's lots of non-functional protein binding to DNA, just see almost any critique of the ENCODE papers for examples.

This is regarding my original question.

What If I find consensus sequences in that region yet still no differential gene expression. So the consensus would imply that this site is preferred by the transcription factor but is still inactive?

I can't rationalize why a transcription factor would be sitting on a promoter region and not affecting transcription.

Where do you find the critiques?

[dpryan]

The presence of a consensus sequence just slightly increases the probability of functionality a bit. Biologically speaking, you need much more than a single transcription factor to have transcription. Firstly, you need accessibility for the rest of the transcriptional machinery (so if you TF doesn't pull in the machinery to do that, then its binding won't do much). Then there's cofactor availability, regulation of other subunits of the transcriptional machinery, etc. There are a lot of moving parts and potential targets for regulation in transcription (not to mention mRNA degradation).