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The best definition to Enhancer and Promoter?
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13 months ago
Shicheng Guo ♦ 7.5k

Is there any deep discussion about the best definition to enhance and promoter?

currently, In my views, promoter is the region from -4000 to +1000 while enhance is -20000 to -4000.

Is there any discuss to such problem? Is there any best definition to promoter and enhance?

chr1 49090 65090 NM_001005484 OR4F5 + Enhancer 69090
chr1 65090 70090 NM_001005484 OR4F5 + Promoter 69090
chr1 69090 69090 NM_001005484 OR4F5 + UTR5 69090
chr1 69090 70008 NM_001005484 OR4F5 + Exon1 69090
chr1 70008 70008 NM_001005484 OR4F5 + UTR3 69090
chr1 70008 72008 NM_001005484 OR4F5 + Downstream 69090
chr1 347658 363658 NM_001005221 OR4F29 + Enhancer 367658
chr1 363658 368658 NM_001005221 OR4F29 + Promoter 367658
chr1 367658 367658 NM_001005221 OR4F29 + UTR5 367658
chr1 367658 368595 NM_001005221 OR4F29 + Exon1 367658
chr1 368595 368595 NM_001005221 OR4F29 + UTR3 367658
chr1 368595 370595 NM_001005221 OR4F29 + Downstream 367658
chr1 347658 363658 NM_001005224 OR4F3 + Enhancer 367658
chr1 363658 368658 NM_001005224 OR4F3 + Promoter 367658

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perhaps in your special case the region containing enhancer and promoter is overlap

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3 months ago
University Park, USA

I would always be cautious to define biological concepts in terms of linear coordinates, the cutoffs are very "human understanding" oriented round numbers that won't generalize well.

When in doubt of what a term means consult the Sequence Ontology:

Enhancer: http://www.sequenceontology.org/browser/current_svn/term/SO:0000165

Promoter: http://www.sequenceontology.org/browser/current_svn/term/SO:0000167

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I didn't know about the sequenceontology.org although apparently has been up since 2009.

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16 months ago
cyril-cros • 890
France

An enhancer does not even have to be on the same chromosome (see http://www.ncbi.nlm.nih.gov/pubmed/16873069 for an example on the monoallelic choice of olfactory receptor WARNING the article had some conclusions invalidated), and can be upstream, downstream, up to 1Mbp away. A promoter is typically in the near cis region of your gene.

The fundamental idea is that RNA polymerase subunits are recruited (or blocked) by a multitude of transcription factors, which can bind to enhancers or promoters, forming a 'mediator complex'.

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I think there is actually a TF/enhancer-interaction protein complex called 'mediator complex'.

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You are absolutely correct, the mediator complex is something else. A better term would be 'transcription initiation complex'.

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13 months ago
Anima Mundi ♦ 2.4k
Italy

Hello, I give you my personal understanding of those concepts. A promoter is the nearest _in cis_ discrete region allowing for ( _promoting_ the) expression of a given gene. Any other discrete sequence _enhancing_ the expression of one or more genes is an enhancer (normally, but not necessarily, _in cis_ ). More general term is regulatory element, comprising any sequence having any kind of effect on the transcription of the gene. Regulatory elements can be _cis_ -acting (e.g. _locus_ control region,LCR) or _trans_ -acting (or, sometimes, both).

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Would agree with that:

A promoter is the nearest (to TSS) _in cis_ discrete region allowing for ( _promoting_ the) expression of a given gene (or genes). Any other discrete sequence (region) _enhancing_ the expression of one or more genes is an enhancer (normally, but not necessarily, _in cis_ ). :-)

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Good specifications, 100% agree!

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2.4 years ago
Ryan Dale 4.8k
Bethesda, MD

As the other answers point out, a genomic distance approach is not useful to define enhancers. A more rigorous definition of enhancers might integrate multiple data sources. For example:

  • Identify regions interacting with promoters in long-range interaction experiments (e.g., Schoenfelder et al. 2015)
  • Since these interactions could be activating, repressive, or nonfunctional, select candidate regions that have enhancer-like chromatin modifications (e.g., from genome segmentation algorithms like ChromHMM)
  • Merge those regions, or cross-reference to see the quality of predictions, with functional assays like those reported in the VISTA enhancer browser
  • For the genes you really care about, you would need to experimentally disrupt the candidate enhancer (e.g. with CRISPR) to see if the candidate region is required for transcription. But even if you get a negative result, it's still possible there are other redundant enhancers, in which case you'd have to disrupt them all!

As for "promoter" definition, it may depend on your question: If you're looking at PolII recruitment, you might benefit from extending the promoter region downstream into the transcript, while focusing upstream would be useful for TF binding. For histone modifications it probably depends on the particular modification.

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