Talk:Non-coding RNA

Untitled
I'm not sure that non-canonical tRNA bases are modified forms of A,C,G,U (like a methylated A), as opposed to just other bases. Anyone know any chemistry?

Info from the gene article to be incorporated "RNA genes are much harder to locate in genome sequences than conventional genes are. Because cells do not translate them, they lack the distinctive ATG codon that heads all protein-coding sequences and guides bioinformatics searches (more at reading frame)." Zashaw 02:57, 24 Aug 2003 (UTC)

hypen
sorry to nitpick, but i'm editing a biology paper for publication and was wondering whether its "noncoding" or "non-coding"? according to dictionary.com, noncoding is a word so it seems the former is the case. also, there exists "noncodingdna.com". if there are no objections, i or (someone else) will move this page to "noncoding RNA" in a few days. Bubbachuck 18:22, 19 July 2005 (UTC)


 * My experience is that both "non-coding RNA" and "noncoding RNA" are used about as often. For example, Google searches for each term in NCBI's site (to eliminate popular press): non-coding vs. noncoding.  Personally, I think "noncoding" sounds ungrammatical (now _I'm_ being pedantic), but clearly people are using it.  As long as one term redirects to the other, I won't complain.  Zashaw 04:38, 20 July 2005 (UTC)

snRNA is not a synonym for non-coding RNA
snRNA (small nuclear RNA) is a class of non-coding RNAs, such as transfer RNA is also a class. But not all non-coding RNAs are snRNAs. Thus snRNA is not a synonym for non-coding RNA --User:AAM | Talk 11:54, 30 March 2006 (UTC)

Prokaryotic or Eukaryotic
I have a question: Of the 6 rRNAs listed (2 mitochondrial and 4 cytoplasmic) which are specific to prokaryotes?

What is a "RNA gene"?
Is the statement, "Nuclear genome contains c.a. 3000 RNA genes (less than 10% of total gene number)." true?

According to the FANTOM project, only 17,594 of the 33,409 transcriptional units were determined to have coding potential. As a result, all remaining units have the potential to be puative ncRNAs [Okazaki et al. (2002) Nature 420:563-573; Suzuki and Hayashizaki (2004) Bioessays 26:833-843]. A very recent estimate suggests that there may be at least 28,000 ncRNAs within the FANTOM library [Liu et al. (2006) PLoS Genet 2:529-536]. Another estimate has put the percentage, at least in humans, at around 98% [Mattick (2001) Embo Rep 2:986-991].

What exactly are you defining as an "RNA gene" in this statement?


 * A gene encoding for RNA (obviously). Might also encode for protein in theory; IONO whether such RNA genes have been found (or been looked for). Dysmorodrepanis 00:28, 24 February 2007 (UTC)

I understand that an RNA gene is a DNA sequence encoding a non-protein-coding RNA, whereas a DNA gene (what people usually are referring to when they say "gene") is a DNA sequence encoding a protein-coding RNA. I think it would be useful to have an "RNA gene" page, that briefly describes the distinction between RNA and DNA genes, lists the described categories (e.g. microRNAs, snoRNAs, tRNAs, etc), and then links to non-coding RNA (rather than redirect). Neuroschizl (talk) 23:17, 13 November 2013 (UTC)

12S rRNA?
What is that? Dysmorodrepanis 00:29, 24 February 2007 (UTC) 12S is correct. due to the unique selective pressure the mitochondrial genome has a 12S and a 16S sequence. The size however is not influential, its the mechanism of action that are important. --Squidonius (talk) 17:47, 11 March 2008 (UTC)

Choices of example non-coding RNAs
Here are some thoughts on the section on types (families) of non-coding RNAs. Firstly I would agree that they are all types of RNA but not that they are all families. Perhaps remove the families part of the title. Also there is inconsitency about the titles. Why use Transfer RNA rather than tRNA? I would suggest that all the titles are given the short form such as tRNA, rRNA, snoRNA etc. Alexbateman 08:06, 10 May 2007 (UTC)

The diversity of RNA
Note: I originally posted this on the RNA talk page. I believe this article could do more to impress upon the reader the amazing diversity (and emerging importance) of RNA. Consider, for a moment, the following:
 * Argonautes and Dicers and known be involved in RNAi-related gene-silencing events in many eukaryotes:
 * scnRNAs: ~28nt siRNAs are specifically expressed during conjugation.
 * microRNAs
 * endogenous siRNAs &mdash; can fall into different classes (based on their biogenesis and function) such as:
 * tasiRNAs (trans-acting short interfering RNAs)
 * natsiRNAs
 * heterochromatic siRNAs
 * snRNAs
 * snoRNAs
 * rasiRNAs (repeat associated siRNA)
 * piRNAs (discovered in 2006 and found to be abundant in developing sex cells. A male animal missing these would be infertile)
 * XIST / Tsix (turns off the second X chromosome in females; see X-inactivation)
 * PINC (pregnancy-induced non-coding RNA)
 * RNAi (aka RNA interference)
 * etc. --Thorwald 01:52, 19 June 2007 (UTC)

Distinction between functional RNA (fRNA) and ncRNA
The term mRNA is used in a confusing way in this section, doesn't mRNA have coding sections by definition? Narayanese (talk) 21:55, 23 December 2007 (UTC)

You're right. My brain must have fallen out when I wrote that section. I replaced mRNA with just plain RNA where appropriate. Cheers. 98.200.147.72 (talk) 05:22, 24 December 2007 (UTC)


 * The Sequence Ontology's definition of ncRNA is also incorrect. The term "ncRNA" is indeed problematic. There are a growing number of RNAs that are known to function on both the RNA and protein level eg. SgrS RNA and RNAIII. Coding, non-coding RNAs? However, in biology there always seem to be exceptions so we generally live with the awkwardness.--Ppgardne 10:46, 25 December 2007 (UTC) —Preceding unsigned comment added by Ppgardne (talk • contribs)


 * Hmm. SO folks are generally very receptive to corrections.  Since SO/OBO_Foundry should be the definitive source for terminology, we can fix this issue in SO and change Wikipedia to match.


 * But what do we do? Option 1 is to treat cases like RNAIII as not ncRNAs (since they are also mRNA) and add fRNA to SO as an umbrella term (ncRNA is_a fRNA, RNAIII is_a fRNA, but RNAIII is not a ncRNA).  Option 2 would be to change the SO definition of ncRNA such that the term fRNA is no longer useful (i.e. ncRNA==fRNA as it is defined on this page).


 * I wonder what the RNA Ontology has to say about this.


 * 71.225.68.14 (talk) 23:26, 28 December 2007 (UTC)

I undid User:Ppgardne's edit of "mRNA" to "RNA" in the opening sentence of this section. The box didn't give me ample room to explain, so I will do it here. The reason is that the sentence is not talking about the general definition of ncRNA, which has already been mentioned in the beginning of the article. It is focusing on the specific case of ncRNA (rather, fRNA) that are on a protein-coding transcript, i.e. mRNA. Indeed, the point of the entire section is discussing whether using "ncRNA" to describe mRNA regions is correct or not, and suggesting fRNA as an alternative. So the term should indeed be mRNA and not more general. 71.225.68.14 (talk) 15:10, 29 December 2007 (UTC)


 * OK, I see your point here. I'm not convinced that it is worth tying yourself up in knots regarding ncRNA vs fRNA terminology. They are essentially synonymous. The fRNA term has the slight disadvantage that it implies that mRNA is not functional (mRNA is not generally regarded to be a ncRNA/fRNA) which I guess is why most people use ncRNA, even though some ncRNAs may also be embedded in a coding RNA. fRNA does have the slight advantage that it includes artificially evolved RNAs eg. SELEX which I guess would not usually be considered ncRNAs. Also, I removed the statement "The Sequence Ontology definition is consistent with the common use of 'ncRNA' in literature", this is your POV. As far as my understanding of ncRNA goes, the SO definition is not consistent with the common use of ncRNA. --Ppgardne 12:46, 30 December 2007 (UTC) —Preceding unsigned comment added by Ppgardne (talk • contribs)


 * BTW, we've been calling many of the functional RNA elements in UTRs and overlapping coding regions Cis-regulatory elements. I added a note to your discussion of UTRs.--Ppgardne 15:38, 30 December 2007 (UTC) —Preceding unsigned comment added by Ppgardne (talk • contribs)

redirecting from "noncoding RNA" and "ncRNA"
I tried searching Wikipedia for phrases/terms "noncoding RNA" (note the lack of hyphen) and "ncRNA", and this page comes up in neither search. Can those two pages be created and redirect to this one, somehow? Thanks. 98.200.147.72 (talk) 05:23, 24 December 2007 (UTC)

Reorganize list
the list is Eukaryote only and a bit too much of a posteriori collection. I propose to put: I think a group large ncRNA for air, xist hotair etc. is in order. Only problem is I am not sure what do proks have! --Squidonius (talk) 18:54, 11 March 2008 (UTC)
 * General
 * rRNA
 * tRNA
 * Prokaryotic
 * sRNA
 * 6S regulatory hairpin
 * so forth
 * Eukariotic
 * miRNA
 * etc.
 * Looks like a better organisation. Go for it. Narayanese (talk) 06:50, 12 March 2008 (UTC)

mRNA doesn't code for protein?
It was formerly believed that the main role for RNA was to code for protein, though there were the recognized exceptions of mRNA (messenger), and tRNA (transfer).

Isn't mRNA precisely the typical type of RNA that codes for protein? Evercat (talk) 14:07, 10 July 2008 (UTC)

Prader-Will

 * "of these a large fraction were found to be alternatively spliced"

Since like every intron-containing gene is alt spliced (Pan, Shai, Lee, Frey, Blencowe 2008), this seems too trivial. Narayanese (talk) 21:08, 15 March 2009 (UTC)
 * Here's a quote from the abstract: "Moreover, these energetically favorable putative targets of HBII-85 snoRNAs are non-randomly associated with genes producing alternatively spliced mRNA isoforms" and from the body of the manuscript "this association of targets with alternatively spliced genes is statistically significant according to the binomial distribution (P-value < 1 × 10− 6)". I could rephrase the sentence to illustrate this better. I haven't read the PSLFB'08 paper. However, if they're using deep sequencing the method is probably extremely sensitive and may pick up many spurious examples.--Paul (talk) 21:33, 15 March 2009 (UTC)


 * They carefully checked for false positives, and Pan and collegues' finding is consistent with previous deep sequencing (Wang, Sandberg et al 2008) and microarray (Pan, Shai, Misquitta 2004; Johnson, Castle et al 2003) results where >70% of genes were alternatively spliced. Narayanese (talk) 04:57, 16 March 2009 (UTC)


 * I guess the key question is how biologically relevant are lots of low levels of alternative splicing events. Fig. 1 panel b of PSLFB'08 shows that the known alt-splicing events are rather frequent, whereas the new ones that they detected are infrequent. There is a distinct possibility that many of these events don't produce functional protein.--Paul (talk) 09:20, 16 March 2009 (UTC)

Biological roles of ncRNA
I changed "Noncoding RNAs are a diverse group of genes involved in many cellular processes" to "Noncoding RNAs belong to several groups and are involved in many cellular processes" because I'm unsatisfied of talking of RNAs and Genes as they were synonyms. Genes are genes, that is DNA, and RNA is a product thereof. You would not say "Proteins are a diverse group of genes" would you?

And yes, you can also call something an "RNA gene" and mean this is a gene that codes for an RNA. But _all and every_ genes code for nothing else than RNA after all. Some RNAs are translated to protein and some not but the genes that they are the product of don't have any influence on this.

91.6.100.238 (talk) 03:47, 28 March 2009 (UTC) MarcoP Berlin

"Functional" and "coding" need clarifying
Could someone please articulate what the words "functional" and "coding" mean in this context, especially the degree of their ambiguity in common usage? Here's the problem:

Intro: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein."

OK, so (a) that implies that "coding" means "code for a protein" (and not "code for anything useful"), and (b) relies on the reader knowing what "functional" means.

Then later in the intro we have "The number of ncRNAs encoded within...". This is actually logical, but needlessly uses "code" in two different senses in the same sentence ("nc"="not-encoding a protein", then "encoded" = "a sequence in the DNA").

The trying-to-be-helpful section "Distinction between functional RNA (fRNA) and ncRNA" says: "Several publications have started using the term functional RNA (fRNA), as opposed to ncRNA, to describe regions functional at the RNA level that may or may not be stand-alone RNA transcripts"

Again, this relies on us knowing what "functional" ("at the RNA level") means.

I infer that "functional" means "able to do something", that is, "a sequence long enough to make sense and to actually perform a *function*". Is that right? Or is "functional" more specific than that? Gwideman (talk) 23:29, 17 May 2013 (UTC)

Not all ncRNAs are functional.
I do not think that the first line "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein" is correct. Just because a non-coding RNA is present it does not mean that it has a function. For now I will not edit this line, but leave this idea out there for discussion. Here is a peer-reviewed article we wrote on the subject: http://journal.frontiersin.org/article/10.3389/fgene.2015.00002/abstract — Preceding unsigned comment added by Microtubules (talk • contribs) 15:32, 11 August 2015 (UTC)


 * I have gone ahead and edited this section.Microtubules (talk) 21:20, 15 September 2015 (UTC)