Transcription Factor Peaks 3' of gene

[Livi81]

Hi,

I'm fairly new to chip seq and I've been given some transcription factor datasets to rummage through. I found some lovely peaks (consistent in 4 different samples) just beyond the 3' end of a really interesting candidate gene (actively transcribed). Are there any examples where TF binding beyond the 3' end of a gene has been shown as functional? Like a 'backward' promoter if you will?

Any suggestions appreciated, apologies if it's a daft question!

Livi

ps. the nearest gene other than my interesting candidate is over 30kb downstream

[flobpf]

Possible

such CREs have been previously documented, mostly in Drosophila. Check out DPP protein and this paper:

http://genome.cshlp.org/content/15/1/1.full

which says
"...Our collection comprised 142 sites over 30 genes, characterized using a variety of experimental methods, ranging from in vitro binding assays to detection of a mutational phenotype. Of these sites, 63% were upstream of their respective gene, 25% were internal to the gene, and 6% were downstream of their respective gene; all of the sites were analyzed...."

The examples are rare because most people dont look for TFBS in the 3'-UTR. But now with genome-wide studies becoming accessible to regular labs, look out for more such examples. you may be having some hot stuff in your hands.

i'm not sure if you can call it a backward promoter (since promoter is where the RNA Pol binds), but one possible mechanism would involve looping of the DNA to activate/repress transcription or some post-transcriptional role for the TF

[Livi81]

Ok, great thanks for your help.

[flobpf]

such CREs have been previously documented, mostly in Drosophila. Check out DPP protein and this paper:

http://genome.cshlp.org/content/15/1/1.full

which says
"...Our collection comprised 142 sites over 30 genes, characterized using a variety of experimental methods, ranging from in vitro binding assays to detection of a mutational phenotype. Of these sites, 63% were upstream of their respective gene, 25% were internal to the gene, and 6% were downstream of their respective gene; all of the sites were analyzed...."

The examples are rare because most people dont look for TFBS in the 3'-UTR. But now with genome-wide studies becoming accessible to regular labs, look out for more such examples. you may be having some hot stuff in your hands.

i'm not sure if you can call it a backward promoter (since promoter is where the RNA Pol binds), but one possible mechanism would involve looping of the DNA to activate/repress transcription or some post-transcriptional role for the TF

it is also possible that there is a yet-undiscovered antisense gene or an anti-sense RNA. yes, that kind of a freak-show.

[steven]

Looking for "widespread antisense transcription" in pubmed and google scholar may give you other interesting references.