miRNA alignment to the genome

Question

[GouthamAtla]

Hi all,

I have not done miRNA data analysis before, I have a small question regarding miRNA read mapping. The miRNAs are generated either by cleaving off from a mRNA or from a translated hairpin structure from a part of genome. They function by complimentary base pairing with mRNA of certain gene.

If we assume that the miRNA generated is from a genomic region, when we align this miRNA reads to the genome, ideally this read should map to the genomic position where it is originated and also to the corresponding exonic region which it is supposed to form a complimentary base pairing. Hence, the miRNA that forms base pairing with mRNA, should map to the two locations in the genome. I would like to know if my understanding is correct.

And also the miRNA will map to the exonic portions of the genome?

Answer 1

[Ashutosh Pandey]

A mature miRNA can map to two or several regions in the genome but not because of the reason mentioned by you above.

Mature miRNAs can recognise their targets by as little as 6-8 nuclleotides (seed region). A global aligner will try to align the mature miRNA (22 nucleotides) fully and will miss the target regions. So, multiple mapping of a mature miRNA against the reference genome is not due to multiple alignments of miRNA against its target genes but because of the reason mentioned below.

Mature miRNAs are initially transcribed as part of a precursor miRNA (primary miRNA). Many different primary miRNAs originating from different regions in genome can be converted to the same mature miRNA after processing. Thats why a mature miRNA can map to different regions in the genome depending on where its precursors were originated.

[GouthamAtla]

Hi Ashutosh,

when looking at the alignment distribution to genomic regions, shud the miRNAs map to genomic ( coding ) regions or it is not necessary that miRNA maps to coding regions ?