Talk:Transcriptome

More than just expression profiling

I think the study of transcriptome involves more than just profiling of expression, but also simple cataloging transcript species, as well as determining their transcript structure (start, end sites), splicing patterns, etc. --Huggie (talk) 06:25, 18 July 2011 (UTC)

From PNA/Biology

• Transcriptome -- this page is just a skeleton with lots of headings and little else. And while the word is a bit dubious, the other xxxome-pages (expressome!? regulatome? give me a break) referenced smack way too much of creative word games. In addition, I don't think the definition is the only one possible; I'm fairly sure transcriptome is used to refer to the set of transcribed sequences, i.e. all the different transcripts produced from a genome. Ketil 2004-11-04
  • Transcriptome is a legitimate, albeit annoying, term in biology and has a place in comparative studies of states (e.g. cancerous vs. 'normal' tissue) and other comparative measures. It's one of those 'omics explosion' terms. Courtland 2005-01-31
  • I spent some time collapsing the lists of links on the several omics pages by introducing the List of omics topics in biology page and cleaning up the several pages it references. I do wish the person(s) who had originally put these up had not been in such a hurry to dash them up then walk away ... or so it seems from my perspective. At the very least they should have been put in as stubbies ... hey, that's not a bad middle ground really. What do you think? Courtland 2005-01-31 (almost 02-01)

Not just mRNA

I think the term "transcriptome" refers to all RNA transcripts, not just messenger RNA. Searching for the term on Pubmed leads to several articles that specifically mention trying to figure what's all that non-coding RNA doing. See also Affymetrix's page on the topic at http://www.affymetrix.com/transcriptome/index.affx, and I guess they should know since that's why their products exist (tracking expression levels). In fact, reading the first paragraph it sounds like the original author intended to mean all RNA transcripts. The last paragraph directly references an article where antisense transcripts are part of the transcriptome. Unless someone objects in the next few days, I'll edit the page to correct this. -Lp 70.81.26.125 16:02, 1 September 2007 (UTC)

Yes, it is a bit confusing in my opinion. I think the more logical definition would refer to all RNA that is transcribed from any gene. Unfortunately the word "transcription" often refers to mRNA mostly; only at a later time was it understood that smaller/shorter RNA plays additional roles in a cell. Perhaps it may be better to add some new term such as RNAome or something like that, to refer to all RNAs, and then reserve transcriptome only for mRNAs. But right now I guess we have to live with the fact that it is not clearly defined, thus leading to possible confusion. 2A02:8388:1604:CA80:7AA0:255D:4602:ABA7 (talk) 17:13, 16 April 2019 (UTC)

redirect from Transcriptomics

I would suggest that the redirect from Transcriptomics should actually lead to Expression profiling since that page puts its focus mostly on the analysis on mRNA expression profiles.--Oleginger (talk) 15:33, 14 August 2008 (UTC)

I agree with this. Are there any objections to making the change now? Jmeppley (talk) 18:38, 5 October 2016 (UTC)

non-coding RNA is not part of the transcriptome

According to T.A.Brown in Genomes 3:

The transcriptome is the set of protein coding RNA (just m-RNA and pre-mRNA). A bit confusing is that trancription gives non-coding RNA as well as the transcriptome. The transcriptome is about 4% of all RNA.

The non-coding RNA is also called functional RNA is not translated into proteins. The most important types of functional RNA are: Ribosomal RNA (rRNA), Transfer RNA (tRNA), Small nuclear RNA (snRNA or U-RNA), Small nucleolar RNA (snoRNA), MicroRNA (miRNA) and short interfering RNA (siRNA)

So I think there are corrections to be made in the article: 1. transcriptome IS just protein coding RNA 2. all others than (pre)mRNA are NON-coding.

2010-04-12, Enschede The Netherlands

I would respectfully suggest that the honorable T.A.Brown is incorrect.--Paul (talk) 21:47, 13 April 2010 (UTC)

Honorable T A Brown here. I think the word ‘transcriptome’ was first used by Bert Vogelstein and Kenneth Kinzler in papers in Cell (88, 243) and Science (276, 1268) in 1997. They did not specify exactly what they meant but reading the papers it is pretty clear they were thinking about the mRNA component of the cell. I wrote the first edition of Genomes just after those papers came out so defined transcriptome as the ‘mRNA content of the cell’. Personally I think that is the most useful definition as it means that the transcriptome is the coding RNA and hence the part of the total cell RNA that specifies the proteome and through that the biochemical capability of the cell. But I’m not an RNA biologist and what is important is what people who study the transcriptome actually think the word means now. I’m not sure though if there is really agreement in the field - for example, a recent paper in Cell is called ‘Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP” (Hafner et al, Cell 141, 129, 2010). That title seems meaningless to me if microRNAs are a part of the transcriptome. Terry Brown. —Preceding unsigned comment added by 86.185.134.42 (talk) 14:48, 17 April 2010 (UTC)

Hi Hon. TA Brown. ;-) I'm basing my argument on the the word Transcriptome, that is Transcipt and -ome - in this context essentially meaning 'of the genome'. I don't see anything specific to protein coding genes there. Just because a few microarray users have been using the term to mean protein coding genes doesn't, IMHO, make it true. I haven't contributed text to this article but I think the existing definition is correct. Especially given that most transcriptome work is now shifting to using RNA-Seq. Which, depending on the sample prep., is unbiased regarding protein coding content.--Paul (talk) 20:33, 18 April 2010 (UTC)

While this makes a lot of sense, I should add that RNA can play a useful role in regards to gene regulation or defence against foreign RNA too. While I understand that mRNA plays the primary role, I would not too easily dismiss other forms of RNA playing a role in this regard. I guess due to the historic reason we have to assume that the transcriptome refers to mRNA only, even though I think it could fit to all DNA that is transcribed into RNA (part of the problem comes from the term itself, e. g. what is exactly meant with a "transcript" as such? People established these terms many years before new roles and functions were discovered). 2A02:8388:1604:CA80:7AA0:255D:4602:ABA7 (talk) 17:16, 16 April 2019 (UTC)

Meiome

The Meiome page has been deleted, I don't know where that was discussed, but it is apparently because somebody claimed it was non-notable. There was a proposal to merge it into Meiosis, where one editor argued that it was not a good fit. (I'll remove that proposal now, since it makes no sense after the Meiome page has been deleted.) The code that was on the page, a bit cleaned up, is as follows (one link is broken, the other doesn't mention "meiome"):

Meiome is the term used in functional genomics for meiotic transcriptome. Meiosis is a key feature for all sexually reproducing eukaryotes, and involves the pairing of homologous chromosome, synapse and recombination. Since meiosis in most organisms occurs in a short time period, meiotic transcript profiling is extremely difficult due to the challenge of isolation (or enrichment) of meiotic cells (meiocytes). Currently there are two major approaches to understand the RNA accumulation in meiocytes: 1) RNA sequencing and 2) microarrays. High-throughput sequencing and microarray technologies can be used.

I'd like to suggest that Meiome could be merged into this page. This isn't my area of expertise, so I don't even know if there are other -ome terms that could be treated similarly. I think these terms belong in wiktionary, but as well as in wikipedia, not instead.

The following references might be useful:

Bovill, W.; Deveshwar, P.; Kapoor, S.; Able, J. (2009). "Whole genome approaches to identify early meiotic gene candidates in cereals". Functional & Integrative Genomics. 9 (2): 219–229.{{cite journal}}: CS1 maint: multiple names: authors list (link) which says "However, with the advent of large-scale transcriptomics approaches such as microarrays, the meiome is beginning to be explored at a whole-genome level."

BMC Genomics. 2006 Oct 19;7:267. Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat. Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA., http://www.biomedcentral.com/1471-2164/7/267/ which says "The resulting data set helps define the wheat meiome (meiotic transcriptome)".

Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. Priyanka Deveshwar, William D Bovill, Rita Sharma, Jason A Able and Sanjay Kapoor, BMC Plant Biology 2011, 11:78 doi:10.1186/1471-2229-11-78 http://www.biomedcentral.com/1471-2229/11/78/ which has a section heading "Towards understanding expression dynamics of the meiome". Sminthopsis84 (talk) 14:01, 5 June 2012 (UTC)

References

Exome

This should say something about the difference between a transcriptome and an exome. — Preceding unsigned comment added by Tedtoal (talk • contribs) 18:56, 13 November 2012 (UTC)

The page needs updating to reflect the greater range of transcription products from DNA, now that the "junk DNA" hypothesis has been overthrown. Sminthopsis84 (talk) 18:41, 14 November 2012 (UTC)

Transcript needs defining

This article introduces the term 'transcript' with no definition or link to a definition. The meaning is not obvious to a layperson and needs defining. 86.137.222.175 (talk) 08:06, 19 November 2014 (UTC)

The link would be to transcription (genetics). I've added that as the link for "transcribed" because I think that might be clearer than linking from "transcript". Sminthopsis84 (talk) 14:25, 19 November 2014 (UTC)

Merge Expressomics page into Transcriptome

"Expressomics" is a deprecated term. — Preceding unsigned comment added by MangoldOrganizer (talk • contribs) 03:07, 25 March 2017 (UTC)

• Agree that merge is logical. In some ways, it might be more logical to merge into transcriptomics (currently transcriptomics technologies). Bias note, I co-wrote the transcriptomics technologies page. T.Shafee(Evo&Evo)^talk 02:43, 23 May 2017 (UTC)

Introns and spurious transcription

I removed a curious and incorrect reference to the Central Dogma of Molecular Biology. More importantly, I added references to spurious transcription and the controversy over how many of the detectable transcripts are functional or junk RNA.

I also made a point to mention introns as an important part of the transcriptome. We should probably include a mention of pervasive transcription since that was a key point of the ENCODE studies.

The history needs to be fixed since the first studies of the transcriptome are the Rot analysis experiments from the late 1960s showing that mRNA was only a small fraction of the total RNA. Other components were known non-coding RNAs and heterogeneous nuclear RNA (hnRNA). Genome42 (talk) 22:12, 12 April 2023 (UTC)