%% so my doubt is that, is it possible that one miRNA can birth from many chromosomes ???

Yes.

It is a great question. Generally, the birth of miRNA should be also due to genome or gene duplication. Yet it can be more complex. It might be interesting to discriminate ohnolog, ortholog, and paralog.

It is a very active research field. Many relevant publications are available.

@Mirey plass: Sorry perhaps, i have not clear my question or you haven't read clearly my NOTE, that i was not concerning isomiRs, i know that nomenclature of miRNAs.

I WANTED TO KNOW THAT, IS IT POSSIBLE THAT ONE miRNA CAN BIRTH FROM MANY CHROMOSOMES ???

like i have found many miRNAs which belongs to many locations,

for example: dre-miR-724 deposited in miRBase belongs to only chro11, however, i have found for same miRNA (mature) in two different location (chr11 and chr8). Moreover, crossed checked by UCSC BLAT given same chromosomal result (chr11, chr8) for the same precursor (find attachment). Only the difference, i have found in my prediction and deposited seq is that my predicted precursors are a little shorter than deposited in miRBase v20.

Thanks for your reply.

@ Yongzhong Zhao: Thank you sir for your answer and explanation. Apart from known, i also have seen same property for novel miRNAs.

So 1) could we referred these miRNAs as copy numbers ????

2) while validating these novel miRNAs, it can have affect in differential expression ?? I mean, assuming single location for each miRNA, we have validated (by RT-qPCR) some predicted novel candidates which were expressed almost in same expression level and further cross checking by UCSC BLAT, we have found many locations for the same precursor miRNAs.

That is why i raised this question !!!!

@Rupesh

I feel both are novel question. It might be necessary to figure out potential duplication history for the copy number claim. Meanwhile, it will be interesting to tackle the differential expression issue yet to get an optimized experimental strategy, for which many issues would be anticipated arsing, such as efficient primer design and how to handle the low level expression of some loci and the complexity of precursors problem. I feel Northern blot or RNA-protecting assay appear to be necessary. It will not be trivial even to be valued as a PhD dissertation project if linked to more mechanisms underlying physiological or pathological functions.

@Yongzhong:

Thank you sir for your opinion from your great experience. One more issue i have to share with you. We have validated 18 Novel miRNAs (mature seq) by using miScript HiSpec Buffer of miScript SYBR Green PCR Kit (QIAGEN,Venlo, Netherland). And all expressed almost same levels as i said before. Therefore, after we have seen not only many locations (at most 3) for the same miRNA gene, also found isomiRs (just 1-2 nucleotides diff). However, someone said, used protocol (qiagen) is not very effective to validate mature RNAs precisely, try to use 'TaqMan' probes (as you also have advised above, to design efficient primer).

However, as far as i know, TaqMan biochemistry is better than qiagen but they also not claimed to discriminate between 1 or 2 nucleotides difference (specially i have in 5').

Could you suggest me something, how to overcome this issue as well ??

Thanks a millions for your time and reply.

To discriminate mature miRNAs with1-2nt differnce, a cost-effective way is to run a non-denaturing PAGE of amplifed PCR products, such as SSCP. Or run NGS if realistic.