Talk:Non-coding RNA

message: 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)
thread_title: Untitled

message: 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)
replies: text: 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)
thread_title: hypen

message: 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)
thread_title:  snRNA is not a synonym for non-coding RNA 

message: 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)
thread_title:  What is a "RNA gene"? 

message: What is that? Dysmorodrepanis 00:29, 24 February 2007 (UTC)
thread_title: 12S rRNA?

message: 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)
thread_title:  Choices of example non-coding RNAs 

message: 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 — 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)
thread_title: The diversity of RNA

message: 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)
thread_title:  redirecting from "noncoding RNA" and "ncRNA" 

message: the list is Eukaryote only and a bit too much of a posteriori collection. I propose to put:
* General
** rRNA
** tRNA
*Prokaryotic
** sRNA
** 6S regulatory hairpin
** so forth
* Eukariotic
** miRNA
** etc.
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)
replies: text: Looks like a better organisation. Go for it. Narayanese (talk) 06:50, 12 March 2008 (UTC)
thread_title:  Reorganize list 

message: 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)
thread_title: mRNA doesn't code for protein?

message: :"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)
replies: text: 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)
replies: text: 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)
replies: text: 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)
thread_title:  Prader-Will 

message: 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)
thread_title:  Biological roles of ncRNA 

message: 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)
thread_title:  "Functional" and "coding" need clarifying 

message: 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)
replies: text: I have gone ahead and edited this section.Microtubules (talk) 21:20, 15 September 2015 (UTC)
thread_title:  Not all ncRNAs are functional.