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I see a lot of different DNA elements mentioned as part of a gene (talking about eukaryotes):

The length of DNA following the promoter is a gene and it contains the recipe for a protein. (video)

This implies that the promotor is not part of the gene.

enter image description here

This actually defines a gene without enhancers/silencers

enter image description here (source)

Here the gene also includes the enhancers/silencers

Question
Is there an accepted gene definition regarding the DNA elements? Thus which sequences like promotors, enhancers, silencers etc. are considered part of the gene?

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  • $\begingroup$ Do you have a use case or that definition, something specific that requires you to have definition, i.e. "if A is gene why B is not"? Also, if I say "gene is X", how will you know if it is good or bad? $\endgroup$ – aaaaaa Mar 2 '17 at 23:51
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Usually a promoter is not considered a part of the gene. Distal regulatory elements qualify even lower for being considered a part of a gene because they can regulate many genes simultaneously.

Basically, a geneic region starts from the transcription start site (TSS) and ends at the terminator (or polyadenylation/cleavage site in eukaryotes). If a gene gives rise to multiple transcripts, those which have similar products (no frameshifts) but different TSS/terminators, we should consider the geneic region as a union of all the primary transcripts produced from that site.

There is a relatively old article on this topic: What is a gene, pose ENCODE? History and updated definition. It summarizes that:

There are three aspects to the definition that we will list below, before providing the succinct definition:

  1. A gene is a genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein.

  2. In the case that there are several functional products sharing overlapping regions, one takes the union of all overlapping genomic sequences coding for them.

  3. This union must be coherent—i.e., done separately for final protein and RNA products—but does not require that all products necessarily share a common subsequence.

This can be concisely summarized as:

The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.

enter image description here.


My summary is that a gene, if it codes for a protein, would be a union of all primary transcripts that produce identical proteins (originating from transcripts with different TSS/terminators) or splice variants. Ideally, all the different transcripts produced from the locus would have the same promoter.

Overall, it appears that a common promoter is imperative for considering the different products under the same gene because if two products are produced from different promoters then we consider them as products of overlapping genes.

Whether we should consider the promoter as a part of a gene is an open debate.

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  • $\begingroup$ While your post is detailed, I'm a fifth year PhD student in genetics and I barely follow it. $\endgroup$ – Artem Mar 17 '17 at 8:48
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    $\begingroup$ @Artem Possibly, you can ask for specific clarification instead of downvoting. $\endgroup$ – WYSIWYG Mar 17 '17 at 8:49
  • $\begingroup$ @WSIWYG. I don't think it's wrong for a textbook answer, I just think it's unclear. What about subsets of non-coding RNA? How much and what kind of non-coding overlap determines a common gene? Or if two non-coding transcripts with the same first exon and different second exons with distinct functions? $\endgroup$ – Artem Mar 17 '17 at 9:19
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    $\begingroup$ @Artem Unfortunately, even the scientific community and the genome consortia have not clearly defined these categories and hence they are unclear. How to differentiate between overlapping genes and a single gene with multiple isoforms? There is no definition out there yet. Usually splice variants are considered under the same gene. If we accept this then it appears that if many transcripts share a common promoter they are considered the product of the same gene. $\endgroup$ – WYSIWYG Mar 17 '17 at 9:34
  • $\begingroup$ @ WYIWSYG What happens if in case #2 and #3 the two genes share just a single amino acid or a single helix? The 'Coding Sequence' would be technically be in the first exon and thus it's the same case as 'A-B' 'A-C' which are the same gene. $\endgroup$ – Artem Mar 17 '17 at 17:08
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It depends. There are two broad definitions which work.

The more common definition of a gene is the transcribed portions of DNA, a gene begins at the transcription start site and ends at the Poly-A site. This is common when discussing mRNA, lncRNA, tRNA. It's what most scientists refer to when they say the ACTB gene or IRF5 gene or something.

If you want to explicitly include all introns you say 'Gene Body', if you want to exclude introns you simply say ' ACTB Exons'.

An older and arguably better definition of the gene from Thomas Morgan is a unit of heredity, that when mutated results in a phenotype.

The second definition doesn't say anything about transcription and would be inclusive of things like promoter/enhancer mutations. From a molecular biology stand-point is more difficult to define. It's more useful for genetics because you're interested in how a phenotype is inherited and it's etiology, not how an a species of RNA functions.

98% of the time when people discuss genes they mean the former definition, but this is still an actively debated issue and as we learn more about genetics it will change.

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