Authoritative genomic regions for Promoter and Enhancer of Human genome

Question

[Shicheng Guo]

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

[Devon Ryan]

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.

[DG]

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.

[Shicheng Guo]

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”

Answer 1

[Giovanni M Dall'Olio]

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

[DG]

Excellent resources

Answer 2

[DG]

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.