Talk:MicroRNA

message: The first sentance states that miRNAs are single stranded molecules. My understanding was that miRNAs were short, double stranded RNAs that were formed after processing of single stranded RNA precursors existing in a stem loop conformation. Please clarify. Thewookie55 20:36, 5 July 2007 (UTC)
replies: text: They are indeed double-stranded for a short while during their biogenesis but one strand (the "passenger") is discarded during maturation. The active form is single-stranded so that it is free to hybridise to the target mRNA. Same for siRNAs by the way. Tospo 09:37, 30 October 2007 (UTC)

text: Pasha could also be a Russian soft variant of the name "Pavel" (Paul), Drosha = Andrusha = Andrey (Andrew). CopperKettle 04:51, 28 February 2007 (UTC)

text: I'm not familiar with piRNAs, but I don't think they're microRNAs (even if they're small).  I think microRNAs are very small RNAs (~22 nucs) that are processed by the dicer enzyme and are antisense to mRNAs.  Perhaps another article should be started on piRNAs?  Zashaw 23:25, 12 September 2006 (UTC)

text: I've learned something today.  (Now I can goof off till tomorrow ;-)  There's already an article Non-coding RNA, which I consider a synonym for small RNA (although "small" in this case means less than say a couple hundred nucs).  What I would propose is a separate article on piRNAs, which would be linked from Non-coding RNA, and probably microRNA.  Or maybe if there's not that much info on piRNAs, then just a paragraph in the Non-coding RNA article.  Seem right?  Zashaw 00:16, 14 September 2006 (UTC)
replies: text:  I didn't know of the article either Zashaw. It could be condensed into a sentence or two for a short concise description. It will fit nicely in the non-coding RNA article (which is shaping up nicely-most excellent) after I quickly gave it a look see. Great call! I have a Science review article talking about piRNA, miRNA, etc. that I could use for a concise sentence or two. It may need its own stub for more detail, but the noncoding article is a great place to tie it all together. GetAgrippa 05:07, 15 September 2006 (UTC)

text: If we have enough content on these RNAs, we should put them in a more specific article.  I haven't been following the literature enough to say what the article should be called.  However, at the moment, the non-coding RNA article seems logical, because (1) we only have a small amount of information on the sh-, pi- and asRNA, and (2) these _are_ non-coding RNAs.  Regardless, an article on Dicer and/or the RISC seems worthwhile, no matter where we discuss things. Zashaw 21:51, 25 September 2006 (UTC)
thread_title:  Older comments 

message: There is already an article for RNA interference. GetAgrippa 20:09, 7 October 2006 (UTC)
thread_title:  RNA interference 

message: I don't know how to use Wiki's tools, please forgive me for little bit inconsistence writing:
"miRNA can be located in different parts of genome. Many miRNAs are found in non-coding regions, like the first identified lin-4 and let-7. On another hand, miRNA can be found in the coding region for the specific protein but encoded in antisence direction. In the later case this miRNA usually silences expression of the protein in the sense direction. Last class of miRNAs, based on their coding location, is intronic miRNAs. Intronic miRNA are located in intronic regions of genes. Although both 3'UTR and 5'UTR can be considered intrones, processing of intronic miRNA located in in-frame intrones varies significantly. Intronic miRNAs have two feature which define their placement into separate group: first, they share the same promoter as a target gene, and second, they must be spliced out of the transcript of such encoded genes befor further processing into mature miRNA."
"It is still disputable if intronic miRNA are processed by Drosha after their respective introne is spliced out. Another alternative could be further processing by splaceosomal components before it is transported out of nucleus. Intronic miRNAs are transported out into cytoplasm where they are cut by Dicer."
Previous two paragraphs are based on Intronic MicroRNA (miRNA), Lin et al.,PMID: 17057362 [PubMed - in process].
"miRNA-mediated post-transcriptional silencing could be achived in two ways. One way is similar to shRNA mechanism when target mRNA is degraded, and another way to achieve translational silencing is to form miRNA-protein-mRNA complex uncapable of binding to ribosomes."
Later I'll add a paragraph or two about Drosha processing and thermodinamical properties of RNA plus folding prerequisites for optimal cleavage by Drosha. I would be really greatful if somebody with deeper understanding of termodinamic properties of nucleic acids would step in and write this part.
Viral vectors is another great tool for gene silencing and a lot of groups now use viral vector delivery of miRNA.
Iralets 17:14, 27 November 2006 (UTC)
thread_title:  suggested paragraphs 

message: Following paragraphs are based on two articles (plus my attempt to compile these findings):
Han, J. et al. Molecular Basis for the Recognition of Primary microRNAs by the Drosha-DGCR8 Complex. Cell, 125, 887-901.
Zeng, Y., et al. Efficient Processing of Primary microRNA Hairpins by Drosha Requires Flanking Nonstructured RNA Sequences. J. Biol. Chem., 280 (30), 27595-27603
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Zeng et al. have shown that efficient processing of pre-miRNA by Drosha requires presence of extended single-stranded RNA on both 3'- and 5'-ends of hairpin molecule. They demonstrated that these motives could be of different composition while their length is of high importance if processing is to take place at all.
Their findings were confirmed in another work by Han et al. Using bioinformatical tools Han et al. analysed folding of 321 human and 68 fly pri-miRNAs. 280 human and 55 fly pri-miRNAs were selected for further study, excluding those molecules which folding showed presence of multiple loops. All human and fly pri-miRNA contained very similar structural regions, which authors called 'basal segments', 'lower stem', 'upper stem' and 'terminal loop'. Based on the encoding position of miRNA, i.e. in the 5'-strand (5'-donors) or 3'-strand (3'-donors), thermodinamical profiles of pri-miRNA was determined. Following experiments have shown that Drosha complex cleaves RNA molecule ~2 helical turns away from the terminal loop and ~1 turn away from basal segments. In most analysed molecules this region contain unpaired nucleotides and deltaG [this triangular letter] is relatively high compared to lower and upper stem regions.
Most pre-miRNAs don't have perfect double-stranded RNA (dsRNA) structure toppled by a terminal loop. There are few possible explanations for such selectivity. One could be that dsRNAs longer then 11 base pairs activate interferon response and anti-viral machinery in the cell. Another plausible explanation could be that thermodinamical profile of pre-miRNA determines which strand will be incorporated into Dicer complex. Indeed, aforementioned study by Han et al. demonstrated very clear similarities between pri-miRNAs encoded in respective (5'- or 3'-) strands.
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There were some works showing that dsRNAs with blunt ends are indeed strong inflammatory agents and the longer they are, the stronger is response.Iralets 13:55, 6 December 2006 (UTC)
thread_title:  efficient processing of miRNA  by Drosha 

message: From Pei, Y. and Tuschl, T. On the art of identifying effective and specific siRNAs. Nature Meth., 3(9):670-676.
siDESIGN http://www.dharmacon.com/
RNAi Designer: http://rnaidesigner.invitrogen.com/
BIOPRDsi: http://www.biopredsi.org
Whitehead siRNA Selection server: http://jura.wi.mit.edu/bioc/siRNA
siDE: http://side.bioinfo.ochoa.fib.es/
siSearch: http://sisearch.cgb.ki.se/
Sirna: http://sfold.wadsworth.org/sirna.pl
siRNA design software: http://www.cs.hku.hk/~sirna
These programs can be used for designing artificial siRNA. —The preceding unsigned comment was added by Iralets (talk • contribs) 14:32, 6 December 2006 (UTC)
thread_title:  siRNA sequence selection web tools 

message: The section on miR-155 seems too long for this general page on microRNAs.  I would suggest that this material is moved to a new page specific for that microRNA. It is probably worth noting that miR-155 is the first one to be knocked out, but perhaps not much more than that. Alexbateman 13:29, 14 May 2007 (UTC)
thread_title:  miR-155 section 

message: I removed this text as a copyright infringement. However, it is sourced and reasonably important, so if someone wants, they can rewrite it.-Wafulz 17:15, 7 August 2007 (UTC)
thread_title:  Copyright infringement 

message: This entire article needs a revamp, there are several issues, mainly in the accuracy of the information provided/or the understanding taken therefrom. I have just completed a PhD solely on miRNAs and would be willing to incorporate accurate, thoughtful information on the topic.
Just to clarify one of the earlier Discussion points, miRNAs are not a subclass of siRNAs!!! They are completely different. The main point to consider is that in mammals, endogenous (generated by the organism itself)siRNAs have not been discovered, but they are present in plants (there is also a dire need to discuss the different classes of siRNA that are present in plants and their inherent differences).
Importantly, miRNAs are produced endogenously in mammals and plants, and now constitute the largest class of posttranscriptional gene regulators. miRNAs use miRISC and siRNAs use siRISC, the absolute components of these complexes are not 100% clarified, and some particular miRNAs are thought to utilise additional factors, although the complexes are typically similar. Except for a couple of rare examples, in which a miRNA causes cleavage of a mRNA, miRNAs only bind with partial complementarity to the target, and direct translational repression and or deadenylation of mRNA. The miRNA seed region (nucleotides 2-8) from the 5' end of the miRNA binds to the mRNA target. For a mRNA to be a predicted target of the miRNA, several criteria have to be considered. Besides the obvious seed region match (2-8nt) (although doesn't have to be perfect), the miRNA should be able to access the 3'UTR of the mRNA (i.e the target site must meet strict thermodynamic criteria to be considered, although it might have a perfect seed match)
One more point, Pasha was named so for Partner of Drosha. As simple as that, there is no conspiracy. Also Pasha was first identified in flies by a yeast two hybrid screen as CG1800, and only termed Pasha after another group realised that it was homologous to DGCR8 (DiGeorge Syndrome Critical Region gene 8) in humans. Both DGCR8 and Pasha are dsRBD (double stranded RNA binding domain) containing proteins that function in concert with Drosha to act as a specificity factor in Drosha directed cleavage of the pri-miRNA
also a mention of intragenic versus intergenic miRNAs, their transcription, regulation of their transcription etc should be considered, and also links to some of the sites that we use, such as targetscan and tarbase, and the miRNA registry. These are great sites.
I think that the article should be divided into: history, classification/nomenclature, biogenesis, function (with tables), examples of cancer related, developmentally related miRNAs, miRNAs as prognostic/diagnostic markers etc etc.
i.e do not mention siRNAs, piRNA etc and provide links to a separate article, it is easy to confuse people with these small (but very different) molecules, and this would provide clarity and prevent confusion
Also, miRNA expression analysis by means of Locked nucleic acid (LNA) whole mount in situ hybridisation [LNA WMISH] is a major breakthrough in miRNA research. Knowing the expression of a miRNA enables the researcher to identify possible candidate targets for furhter analysis. see Tuddenham et al (2006) for a good example of mouse LNA WMISH for miR-140.88.111.112.151 (talk) 20:46, 28 November 2007 (UTC)
thread_title:  General notes 

message: (I am not a science wiz, I just like to read it, so sorry if I'm not saying things right and making too much sense!)
I read about this research that showed how this scientist was able to make cancer metastasize and then fully reverse the process by increasing the amount of just one miRNA. The link is below:
http://web.mit.edu/newsoffice/2007/cancer-link-0927.html
I think that it would be worth mentioning in the "miRNA and cancer" section. What do you guys think?  —Preceding unsigned comment added by Believr4god (talk • contribs) 08:19, 2 April 2008 (UTC)
thread_title:  miRNA and cancer section 

message: Until there is much more evidence than one paper on X-linked mental retardation, the article should not say miRNA differences underlie differences in human "intelligence." MiRroar (talk) 16:10, 29 April 2010 (UTC)
thread_title:  miRNA and "intelligence" 

message: I reverted two edits by User:Tinz that helpfully referred to an August 12, 2010 paper by Guo et al in Nature. This paper from David Bartel's lab is important work that will hopefully move us to resolving the debate about relative contributions of translation inhibition and transcript degradation to miRNAs' effects on protein production. However it is probably not ideal to present the debate as settled by this one paper. There are many researchers in the field who collegially disagree with Bartel, and the field has historically viewed inhibition of translation as the main mechanism for miRNA-mediated effects. For many years, one of the things reviewers insisted on in miRNA article submissions was a demonstration that protein levels changed without concomitant changes in mRNA levels. Possibly these researchers were wrong, but it is good to present the debate and not just the latest research article. 
The Guo paper is in an influential journal and maybe we could use it even though it is not a review article, in context of a discussion of the general debate. MiRroar (talk) 14:38, 20 August 2010 (UTC)
replies: text: ok, I can understand you points, probably my addition was premature. Even though the claims in the article are quite strong, and usually only exceptional results appear in the form of an article (not:letter) in Nature. Maybe we can agree to add a sentence that says 1) that there is a debate on this question [because even that doesn't become clear right now], 2) as you mentioned, that for some years consensus was that translational inhibition dominates and 3) that this view is currently being challenged, e.g. by Guo et al. We could replace the citation of the article with a review that discusses its results at a later point, or remove it if - which I doubt - most future reviews ignore it. But those reviews have to be written first. --Tinz (talk) 17:50, 20 August 2010 (UTC)
replies: text: Thank you, Tinz, these are good suggestions. New reviews are best, but it would be ok to contrast past reviews with the new report (or reports, the Bartel lab has several papers on this now.) MiRroar (talk) 20:34, 24 August 2010 (UTC)
thread_title: Translation inhibition versus transcript degradation

message: Why does the mircoarray article link
MMChip to this page "Cellular functions"? There is no mentioning of screening/chip technologies, unless I'm mistaken. Should it link to the section "Experimental detection and manipulation of miRNA"? There is mentioning of microarray, but NO mention of MMChip (and why it is called MM).
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#REDIRECT MicroRNA#Cellular functions
Retrieved from "http://en.wikipedia.org/wiki/MMChip"
Categories: Redirects with possibilities
87.234.43.130 (talk) 15:44, 8 October 2010 (UTC)
thread_title:  Link from MMChip 

message: Hi, editors of this article´s section on "miRNA and the nervous system" !: I´m not a specialist in this topic, nor related ones, but I found this recent news that I believe could be of interest to you, if you want to trace the news up to its roots. 
BTW, an article on Mir-29 microRNA precursor (not on mir-29 itself) already exists in Wikipedia, if you want to reference it.
Pmronchi (talk) 03:23, 19 January 2011 (UTC)
thread_title:  News on mir-29 and neuron´s apoptosis: New molecule could save brain cells from neurodegeneration, stroke 

message: In the section about the RNA-induced silencing complex (RISC) there are a number of citations of the form (authorname, year). At least one of these citations, (Okamura et al, 2008), has no other information (PMID, DOI, even journal name) to help someone find the article referenced.  I believe I have found the referenced article at http://www.ncbi.nlm.nih.gov/pubmed/18769156, but currently don't have the time to learn wikipedia's style conventions. Perhaps someone else can link this appropriately.  —Preceding unsigned comment added by 67.167.138.77 (talk) 13:07, 26 January 2011 (UTC)
replies: text: Should be fixed now.--Paul (talk) 15:01, 26 January 2011 (UTC)
replies: text: Sweet, thanks!  —Preceding unsigned comment added by 67.167.138.77 (talk) 05:12, 27 January 2011 (UTC)
thread_title:  Okamura et al reference 

message: In contrast to stated in the article, microRNA are found in algae.
ref:
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.
Molnár A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC.
Nature. 2007 Jun 28;447(7148):1126-9. Epub 2007 May 30.
PMID:    17538623  — Preceding unsigned comment added by 194.90.153.50 (talk) 12:08, 5 October 2011 (UTC)
thread_title:  microRNA in alga 

message: Unfortunately I don't have access to this review, but perhaps someone who does would like to mine it for information for this page and other non-coding RNA pages. Yesterday I put another new reference on the H19 talk page concerning that gene's microRNA and osteoarthritis. Biochem Biophys Res Commun. 2012 Feb 24;418(4):587-91. Epub 2012 Jan 27. MicroRNAs regulate osteogenesis and chondrogenesis. PMID: 22306817
cheers!Celia Kozlowski (talk) 10:23, 1 May 2012 (UTC)
thread_title:  MicroRNA in bone and cartilage... and autoimmunity 

message: *
Is this already covered in the article? —Pawyilee (talk) 04:51, 15 December 2013 (UTC)
thread_title:  Mathematicians resolve decade-old debate 

message: The past tense of cleave is normally clove, and the participle is cloven.  Is there a good reason to use "cleaved"?  It looks awkward, as would "weaved."
64.40.54.11 (talk) 03:53, 28 October 2014 (UTC)
replies: text: These are two etymologically unrelated verbs that are homonymic despite also being almost antonymic. (FML, right?) They are cleave meaning "to adhere" (intransitive) and cleave meaning "to split" (in both transitive and intransitive senses). For both of the homonyms, the principal parts have variation that is widely accepted (as shown in major dictionaries), but for the "split" verb, they tend toward the strong (irregular) forms—cleave, clove, cloven/cleft. A good way to remember that is to think of established terms such as cleft palate and cloven hoof (both are body parts that are split into two parts). Meanwhile, for the "adhere" verb, the conjugation tends toward the weak (regular) forms—cleave, cleaved, cleaved. The strong forms are sometimes used, but The Chicago Manual of Style in its section "Good usage versus common usage" suggests sticking to the regular forms for the "adhere" verb (which is to say, cleaving to them—har har har). Regarding how dictionaries handle homonyms: notice how Wiktionary has one headword with multiple headings ("Etymology 1" and "Etymology 2"), whereas Merriam-Webster and American Heritage handle them via multiple headwords with numbers (e.g., 1cleave and 2cleave). As for nearly antonymic homonyms, they're almost as fun as speciously antonymic synonyms. Inflammable means flammable? What a country. Quercus solaris (talk) 23:35, 28 October 2014 (UTC)
replies: text:  I forgot to add last night that I suspect that in this context (a microbiological context) it may be difficult to convince microbiologists to stick to the strong principal parts, even though the "split" sense is meant, simply because microbiology today is so thoroughly globalized an effort, with so many ESL participants speaking International English, and so many of them are going to tend to use the weak (regular) inflections, to the point that those inflections may even outnumber the strong (irregular) inflections in the literature on this subject—at which point, it would be a lost cause, editorially, to try to call the regular inflections "wrong" when used within this context. One could still prescribe strong-only in editing work, but it would be a usage preference rather than a correction of an error. Quercus solaris (talk) 21:47, 29 October 2014 (UTC)
thread_title:  Grammar Question 

message: I added a section under "Nervous System" about miRNAs and their possible role in addiction, under the related diseases subheading, which had very little about neurological diseases associated with MicroRNA. I discussed the possible roles of microRNAs in the pathophysiology of alcohol addiction. I also added a sentence to the section about nervous system disorders relating to microRNA function, about how bipolar disorder/depression/anxiety are also related to microRNA function (and not just schizophrenia). Jbryfonski (talk) 00:26, 10 December 2014 (UTC)
thread_title: miRNAs and Alcoholism

message: Within this diagram: https://upload.wikimedia.org/wikipedia/commons/a/a7/MiRNA.svg
The "Base mismatch" just to the right of step 2 is very poorly labelled. 
It is very difficult to see that nucleotide on the Passenger strand has a rounded end, due to the placement of the line from the "Base mismatch" label.Jkokavec (talk) 10:42, 5 March 2015 (UTC)
thread_title:  Diagram depicting miRNA 

message: Hello fellow Wikipedians,
I have just added archive links to  on MicroRNA. Please take a moment to review my edit. If necessary, add  after the link to keep me from modifying it. Alternatively, you can add  to keep me off the page altogether. I made the following changes:
*Added archive http://web.archive.org/web/20080906195601/http://genomebiology.com/2004/5/9/R65 to http://genomebiology.com/2004/5/9/R65
*Added archive http://web.archive.org/web/20110514000250/http://www.aacr.org/home/public--media/aacr-press-releases.aspx?d=2068 to http://www.aacr.org/home/public--media/aacr-press-releases.aspx?d=2068
*Added archive http://web.archive.org/web/20150827183007/http://elifesciences.org:80/content/4/e05005 to http://elifesciences.org/content/4/e05005
When you have finished reviewing my changes, please set the checked parameter below to true to let others know.
Cheers.—cyberbot IITalk to my owner:Online 23:48, 27 February 2016 (UTC)
thread_title:  External links modified 

message: miRNA stem-loops, constituted of palindrome nucleobases with few non palindromic mistakes that cause bending, is a plausible candidate for the mother genotype because it's close to the nucleus (the dwelling place of our genome), it represents both monoclonal RNA and biclonal DNA, it can occur naturally due to statistics and number theory itself. All we need is to build an open virus including supporting proteins. Open viruses are primitive viruses that cannot enclose inside them their genome. Cells with membranes without DNA can occur naturally if enough lipids and stirring are present. It seems that an "open virus" having miRNA stem-loops entered inside some agenetic lipid cell. An open virus is a list of things in a soup, not an enclosed mechanism. It is something very archaic and it's functional only at large numbers, not sufficient as a complete mechanism. It's something random, that inside a vast range of randomness produces also a puny functional result, simply because that's what randomness dictates. Then the mechanism prevails over randomness due to efficiency.
::We know that the ultimate ancestor was a soup, not a single organism, and that soup was comprised also of many genetic-code strands.
:::Soups don't have barriers• so we all are the offspring of a "single organism" called Earthling soup, and thus of common origin. (talk) 19:01, 8 May 2016 (UTC)
replies: text: Bacteriophage genomes may encode as few as four genes (and as many as hundreds of genes). Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. We should build an open bacteriophage (primitive virus not able to enclose its genome) which has miRNA genome in order to probe possible archaic biomechanics.  06:11, 10 May 2016 (UTC)
thread_title:  MicroRNA stem-loops and the origins of life 

message: There is no scientific, WP:RS evidence that miRNAs accumulate from the diet or causes prostate cancer. An IP editor has been adding a citation from a vanity journal to support this claim (IP from the same location as the article's authors), but obviously this addition is not encyclopedic. I have deleted it but could use some help with maintaining the article. Thanks, Rbleibenusw (talk) 03:04, 6 June 2016 (UTC)
thread_title: Vanity press source

message: Seven of the articles cited in this page have been either flagged with an expression of concern, or have their experimental data publicly questioned on Pubpeer : references 104, 134, 137, 161, 185 and 186. They should be removed from the page, as the papers cannot be relied upon. 134.214.242.142 (talk) 13:49, 31 March 2023 (UTC)
thread_title:  Questionable references