Question: Authoritative genomic regions for Promoter and Enhancer of Human genome
1
gravatar for Shicheng Guo
3.4 years ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

Hi,

Do you know which is the most Authoritative genomic regions for Promoter and Enhancer of Human genome? 

 

I don't like the definition of promoter : 5K upstream of TSS

                                         Enhancer: 10K upstream of Promoter

 

Thanks

promoter enhancer • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Dan Gaston7.1k • written 3.4 years ago by Shicheng Guo7.4k
1

These end up changing in every cell type and developmental stage. The "definitions" you posted were never intended to be anything more than vague generalizations.

ADD REPLYlink written 3.4 years ago by Devon Ryan89k
1

Yes, I wouldn't even call them definitions. They are more the distance within which you expect to find promotor and enhancer sequences in general. 

ADD REPLYlink written 3.4 years ago by Dan Gaston7.1k

Yes. Promoter is cell specific. However, it can be considered as a promoter if it is defined as promoter in any kind of cell, I think. That means promoter would be a "union set" rather than “intersection set”

ADD REPLYlink written 3.4 years ago by Shicheng Guo7.4k
4
gravatar for Giovanni M Dall'Olio
3.4 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

A good dataset of gene promoters come from the FANTOM5 project:

- http://fantom.gsc.riken.jp/5/data/

Their data is mainly derived with the CAGE technology, which sequences the first bases of a mRNAs.

Recommended readings:

RIKEN5 consortium. A promoter level mammalian expression atlas. Nature 2014 http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html

RIKEN consortium. An atlas of active enhancers across human cell types and tissues. Nature 2014. http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Giovanni M Dall'Olio26k

Excellent resources

ADD REPLYlink written 3.4 years ago by Dan Gaston7.1k
1
gravatar for Dan Gaston
3.4 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

There isn't a genome-wide authoritative truth set. We know the absolute promoter and some enhancer sequences for some genes. We also have some evidence for where promoter and enhancer sequences may be based on things like DNAse I hypersenstive sites, transcription factor binding experiments, etc. 

ADD COMMENTlink written 3.4 years ago by Dan Gaston7.1k
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