You should read these papers, especially the third talking about mirtrons:
Coding or non-coding: Need they be exclusive?
Francastel C, Hubé F.
Biochimie. 2011 Nov;93(11):vi-vii. No abstract available.
PMID: 21963143
Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events.
Ulveling D, Francastel C, Hubé F.
Biochimie. 2011 Nov;93(11):2024-7. Epub 2011 Jun 26.
PMID: 21729736
When one is better than two: RNA with dual functions.
Ulveling D, Francastel C, Hubé F.
Biochimie. 2011 Apr;93(4):633-44. Epub 2010 Nov 24. Review.
PMID: 21111023
Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation.
Hubé F, Velasco G, Rollin J, Furling D, Francastel C.
Nucleic Acids Res. 2011 Jan;39(2):513-25. Epub 2010 Sep 19.
PMID: 20855289
Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of coding and noncoding RNA isoforms in breast cancer cell lines.
Hube F, Guo J, Chooniedass-Kothari S, Cooper C, Hamedani MK, Dibrov AA, Blanchard AA, Wang X, Deng G, Myal Y, Leygue E.
DNA Cell Biol. 2006 Jul;25(7):418-28.
PMID: 16848684
The steroid receptor RNA activator is the first functional RNA encoding a protein.
Chooniedass-Kothari S, Emberley E, Hamedani MK, Troup S, Wang X, Czosnek A, Hube F, Mutawe M, Watson PH, Leygue E.
FEBS Lett. 2004 May 21;566(1-3):43-7.
PMID: 15147866
The evolution of RNAs with multiple functions.
Dinger ME, Gascoigne DK, Mattick JS.
Biochimie. 2011 Nov;93(11):2013-8. Epub 2011 Jul 23.
PMID: 21802485
Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
Dinger ME, Pang KC, Mercer TR, Mattick JS.
PLoS Comput Biol. 2008 Nov;4(11):e1000176. Epub 2008 Nov 28. Review.
PMID: 19043537
It's a definition problem. lncRNA are defined as bigger than 200 nucleotides.
miRNA are about 20-25 nucleotides and the pre-miRNA are bigger than that, but I don't think that the pre-miRNA can become larger than 200 nucleotides.
Hi ... Ashraf.. I agree with Ali... just a few words to add: these lincRNAs must have more than 200 nt in their physiologically relevant forms (active forms). Since pri and pre miRNAs are not functional units (until now, at least)... they are not considered as lncRNAs or lincRNAs...
As stated above, so no relation - based on the size of functional form.
What about a pre-miRNA encoded in a lncRNA, such as human miR-155 and BIC? The question could be: how many miRNAs are coded into lncRNAs? And also, can pre-miRNA function as a lncRNA?
Andrea ... Always good observations and comments!... In fact the proto-oncogene BIC is currently annotated as the primary transcript for miR155. In this case the pri-miRNA is a lncRNA. However it will only function as a lcnRNA if the encoded miR155 is not processed. If so, the Drosha activity will cleave the lncRNA. This is a very interesting situation of dichotomic functions of the same transcript.
Probably is not a unique case. Other similar situations will eventually exist,.
I must say Francisco you also have good observation and comments about microRNA and lncRNA stuff!
Francesco, you are right. We should investigate more deeply such an interesting dichotomic behaviour, also from a computational point of view.
Andrea ... A few years ago I did a in silico genomic study to detect alternative spliced forms in the human genome containing possible new miRNAs ... I think that I must show the results to you to know what do you think about. It has never been published.. because the "lack of interest" at the time.
Let's say that you have a lincRNA or a coding RNA that contains a miRNA within its sequence. If the miRNA is within a exonic region that means that the processing by Drosha will abolish the transcript activity and functions. Are we looking at an additional way of controlling transcript levels and functions ?... I will appreciate your comments... I have postulated that during a Keystone meeting about ncRNAs. I got many supporting opinions, but also some people that thought that I am crazy.... Should I go to the psychiatrist ?
Francisco, I dont think so you or any researcher who thinks out of the box needs to go to the psychaitrist!!!
But if we accept your concept of miRNA in exonic region, then have you imagined what would decide if that coding region would complete the process of transcription-translation and mature into protein or will just get processed by Drosha and follow miRNA maturation steps?
I dont know if I put my question correctly, but what I am curious to know is in which condition such transcripts will develop into protein, or express miRNA?
Hi Ahsraf... In fact that's the key question (you already put the question perfectly) but I am afraid that nobody knows that ... So it will be extremely cool to join efforts and to look at that !
I am so happy that you consider that I am not in a serious condition ... :)...
Hi Francisco,
Did you already identified miRNAs in coding region? Any known or all novel?
You should read these papers, especially the third talking about mirtrons:
Coding or non-coding: Need they be exclusive?
Francastel C, Hubé F.
Biochimie. 2011 Nov;93(11):vi-vii. No abstract available.
PMID: 21963143
Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events.
Ulveling D, Francastel C, Hubé F.
Biochimie. 2011 Nov;93(11):2024-7. Epub 2011 Jun 26.
PMID: 21729736
When one is better than two: RNA with dual functions.
Ulveling D, Francastel C, Hubé F.
Biochimie. 2011 Apr;93(4):633-44. Epub 2010 Nov 24. Review.
PMID: 21111023
Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation.
Hubé F, Velasco G, Rollin J, Furling D, Francastel C.
Nucleic Acids Res. 2011 Jan;39(2):513-25. Epub 2010 Sep 19.
PMID: 20855289
Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of coding and noncoding RNA isoforms in breast cancer cell lines.
Hube F, Guo J, Chooniedass-Kothari S, Cooper C, Hamedani MK, Dibrov AA, Blanchard AA, Wang X, Deng G, Myal Y, Leygue E.
DNA Cell Biol. 2006 Jul;25(7):418-28.
PMID: 16848684
The steroid receptor RNA activator is the first functional RNA encoding a protein.
Chooniedass-Kothari S, Emberley E, Hamedani MK, Troup S, Wang X, Czosnek A, Hube F, Mutawe M, Watson PH, Leygue E.
FEBS Lett. 2004 May 21;566(1-3):43-7.
PMID: 15147866
The evolution of RNAs with multiple functions.
Dinger ME, Gascoigne DK, Mattick JS.
Biochimie. 2011 Nov;93(11):2013-8. Epub 2011 Jul 23.
PMID: 21802485
Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
Dinger ME, Pang KC, Mercer TR, Mattick JS.
PLoS Comput Biol. 2008 Nov;4(11):e1000176. Epub 2008 Nov 28. Review.
PMID: 19043537
Thanks for the post Florent !....Sounds that I have a lot to read.
It is semantic debate. If you considered that non coding RNA have a role as a RNA form, then pri-miRNA are lncRNAs, which are maturated to be be functional. They indeed are transcribed as lncRNA and have a function as a matured shorter RNA...
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