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In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as.

It seems that it could be defined as the difference in pre-mRNA between the transcription and translation, is that right?

If so, does the transcription begin immediately after the end of the promoter sequence? Immediately after the promoter region on the DNA ends, does the next nucleotide become part of the 5'UTR?

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Concise Answer

The 5′-UTR region of a eukaryotic mRNA is derived from the RNA transcript of the region of a gene between the transcription start site and the DNA corresponding to the translational initiation codon. It differs from that region of the initial transcript in most cases by having a modified guanosine nucleotide added at the 5′-end in a ‘cap’ structure, and in some cases by lacking an intron present in the former.

The Transcriptional Start Site (TSS) and the Promoter

This answer is in terms of the TSS rather than ‘promoter region’ or ‘promoter sequence’, favoured by the questioner because in eukaryotes, at least, there is no simple and easily definable promoter sequence. A 2012 review of metazoan promoters begins with the definition: “Gene promoters are the loci overlapping transcription start sites (TSSs), at which the total regulatory input of a gene is integrated into the rate of transcriptional initiation. The immediate role of the promoter is to bind and correctly position the transcription initiation complex…”.

A simplified diagram of some components of human promoters (adapted from an earlier review by Hahn) is shown below. The position of ‘Inr’ — the Initiator box which contains the TSS — varies with respect to the TATA box (usually from –25 to –30 in humans), as does its sequence. Hence, even ignoring the alternative TSSs mentioned by @Luke it is not possible to identify the TSS unequivocally by inspection of the DNA sequence of a gene in the way the questioner would apparently wish.

Elements in a eukaryotic promoter

The Translational Initiation Codon

It should be mentioned that it also not possible to identify the mRNA translational initiation codon unequivocally by inspection of the DNA sequence of a gene. Although 90% or more cases follow Kozak’s rule, so that it corresponds to the first ATG, in some cases it may correspond to the second ATG, and in a small minority — where internal initiation occurs — to some distal ATG. There are also a very few examples of initiation of translation at codons other than AUG.

Introns in 5′-UTR regions of pre-mRNA

A common rationalization of the intron/exon nature of eukaryotic pre-mRNA is in terms of alternative splicing to produce different protein sequences. Perhaps because of this, the presence of introns in the primary transcript containing the 5′- and 3′-UTRs is often ignored (see Bicknell et al. for a review). In fact, approximately 35% of 5′-UTR precursors contain introns, not present in the mature mRNA.

5′-capping of eukaryotic mRNA

The vast majority of eukaryotic mRNAs have a cap at their 5′-end, produced by the addition of a guanosine nucleotide in a 5′-5′ pyrophosphate linkage to the 5′-residue (usually A) of the pre-mRNA. This is subsequently methylated at carbon-7; and 2′-O-methylation of the ribose of the subsequent one or two nucleotides may also occur.

5'-cap of eukaryotic mRNA

Footnote

Although “DNA makes RNA makes Protein”, I do think it important to describe features of information molecules in terms of their actual composition. Thus, the 5′-UTR has to be defined in terms of mRNA, not promoters or exons. If one makes reference to the information content of DNA or RNA than I think a form of words should be used to make that clear. Muddled forms of words can easily lead to muddled thinking.

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Short answer

The 5' UTR on the mRNA includes sequence from the Transcriptional Start Site (TSS) to the first exon. Promoters are usually associated with a corresponding TSS.

Longer answer

In defining a UTR we must consider where transcription begins. Strictly speaking transcription begins at the Transcriptional Start Site (TSS). A useful website for exact definitions for terms such as this is the Sequence Ontology - see here for the TSS definition (link) - although admittedly in this case it does not provide more information than that (i.e. the TSS is where transcription begins... which we might have gathered from the name). TSS will have an associated promoter region, which is where the RNA polymerase (and various regulators and transcription factors bind).

To expand: a gene may have multiple TSS' which may be promoted under different circumstances (e.g. with different factors present). We therefore have the concept of a TSS region "The region of a gene from the 5' most TSS to the 3' TSS" (link). TSS have to be empirically determined, and seem to vary by tissue (a database of all known TSS has been accumulating evidence since 2002: DBTSS). I have just performed a search for gene APOE (chr 19) and this is a small excerpt of the data presented, just to give an idea:

APOE TSS from DBTSS

From DBTSS

So the TSS for a gene is context dependent on the when/where the transcript is being produced.

In searching for further information I found a paper that describes the 5' UTR on the mRNA, which is not necessarily an exact copy of the genomic DNA (e.g. by addition of the cap). Here is the corresponding paragraph and diagram, which explains it better than I can paraphrase (highlighting by me):

Transcriptional control is mediated by transcription factors, RNA polymerase and a series of cis-acting elements located in the DNA, such as promoters, enhancers, silencers and locus-control elements, organized in a modular structure and regulates the production of pre-mRNA molecules, which undergo several steps of processing before they become functional mRNAs. Introns are removed, a 7-methyl-guanylate (m7G) cap structure is added at the 5' end of the first exon, and a stretch of 100-250 adenine residues (the poly(A) tail) is added at the 3' end of the last exon, which is itself generated by endonucleolytic cleavage of the primary transcript. Sometimes the sequence of the mRNA is also altered in a process called mRNA editing, and the resulting coding sequence of the mature RNA differs from the corresponding sequence in the genome. The resultant mature mRNA, in eukaryotes, has a tripartite structure consisting of a 5' untranslated region (5' UTR), a coding region made up of triplet codons that each encode an amino acid and a 3' untranslated region (3' UTR). Figure 1 shows these and other features of mRNAs.

Mignone 2002. Figure 1

Figure 1: The generic structure of a eukaryotic mRNA, illustrating some post-transcriptional regulatory elements that affect gene expression. Abbreviations (from 5' to 3'): UTR, untranslated region; m7G, 7-methyl-guanosine cap; hairpin, hairpin-like secondary structures; uORF, upstream open reading frame; IRES, internal ribosome entry site; CPE, cytoplasmic polyadenylation element; AAUAAA, polyadenylation signal.

Reference: Mignone, F., Gissi, C., Liuni, S., & Pesole, G. (2002). Untranslated regions of mRNAs. Genome Biology, 3(3). http://www.ncbi.nlm.nih.gov/pubmed/11897027

Promoters

To conclude my answer (apologies for its lack of brevity) there are different types of promoter, not all of which directly include a TSS, but the majority of promoters are called "Major promoters" and do include the TSS (in addition to the RNA polymerase binding site, and other transcription factor binding sites).

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  • $\begingroup$ Well I guess it's just not as simple as I had hoped, but I feel like now I have more questions than I started with. Thank you for such a really thorough answer. $\endgroup$ – Ryan Ward Apr 6 '16 at 22:40
  • $\begingroup$ Thanks for accepting it so quickly - I've updated it some more as I realise it was quite long and hadn't quite answered you question. Included more info on the promoter aspect. :) $\endgroup$ – Luke Apr 6 '16 at 22:42
  • $\begingroup$ You state in your summary that "The 5' UTR on the mRNA includes sequence from the Transcriptional Start Site (TSS) to the first exon". But this is surely wrong as exons are those parts of the transcript that appear in the mRNA, so the 5'-UTR will include the first exon (at least). Indeed, that is what appears in bold in the piece you have quoted. $\endgroup$ – David Apr 11 '16 at 16:58
  • $\begingroup$ Since there are genes with different transcriptional start sites regulated by different promoters, it would be interesting to see if the resulting differences in 5' UTR are used to regulate expression of the mRNAs. This could allow an extra layer of regulation, such that gene X not only needs promoter Y, but micro RNA Z to function, but when promoter W is used, the 5' UTR is different and RNA Z is no longer needed. $\endgroup$ – user137 Apr 12 '16 at 0:58
  • $\begingroup$ Hi @David - maybe I've also misunderstood something but the exons by definition are the translated regions, therefore would not be part of the UTR (un-translated region). On the diagram you can see there is a long stretch of sequence between the start of the mRNA (the cap) and the "coding sequence" i.e. the exons (bear in mind introns have been removed by this stage so all included exons appear together). -- user137 that would be interesting, and I expect it would affect pre-mRNA processing to some degree. $\endgroup$ – Luke Apr 12 '16 at 9:01
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The UTR is the region of the transcript upstream of the starting methionine. The promotor is not itself transcribed.

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    $\begingroup$ Sorry to push the issue, but I don't feel like you answered my question. This is exactly how the book phrases it as well. Is it everything after the promoter but before the methionine? $\endgroup$ – Ryan Ward Apr 6 '16 at 20:20
  • $\begingroup$ In other words, does transcription start immediately where the promoter ends? $\endgroup$ – Ryan Ward Apr 6 '16 at 22:19
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    $\begingroup$ DPEs can be in the transcribed region. biology.stackexchange.com/q/38783/3340 $\endgroup$ – WYSIWYG Apr 7 '16 at 8:09
  • $\begingroup$ @WYSIWYG It seems like there are no hard and fast rules. Thanks for finding that, it pretty much answers my original question. $\endgroup$ – Ryan Ward Apr 7 '16 at 15:37

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