Question

Rna-Seq And Pri-Mirna

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13.1 years ago

Nicolas Rosewick 11k

Hi everybody,

Is it possible to detect pri-miRNA from RNA-seq ? In the literature, I have not found papers talking about such thing.

Thanks,

N.

rna mirna • 4.1k views

ADD COMMENT • link updated 10.3 years ago by Biostar 20 • written 13.1 years ago by Nicolas Rosewick 11k

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any news on your experiments?

ADD REPLY • link 13.0 years ago by Michael 55k

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the experiment is on is way. Answers in january ;)

ADD REPLY • link 12.9 years ago by Nicolas Rosewick 11k

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you didn't say which year ;)

ADD REPLY • link 11.2 years ago by Michael 55k

score 1 · Answer 1 · 2011-09-16

The problem with primary transcripts is that they are processed and degraded, these portions not very likely to yield high coverage in sequencing. They might appear as a weak signal surrounding the mature miRNA. If you know a true miRNA location, one could look for weaker signals surrounding it. If the miRNA is transcribed from an intron, I see marginal chances for separating the signals at all from the background.

score 1 · Answer 2 · 2011-09-16

What Michael says is true, but you might have better luck if you design an experiment that gives you a better chance of finding what you're after.

For instance, as part of their work on the ENCODE project, Tom Gingeras' group has run RNA-seq on different sub-fractionations/sub-compartments across different cell lines. They have all different combinations of polyA+ and polyA-, long, and short RNA isolated from cytoplasm, nucleus, nucleolus, etc.

Perhaps you'll have better luck looking at RNA taken from within the nucleus to get what you are after. Unfortunately I can't link directly to the page for this project since their web-site is in (poorly written) flash, but just go to the lab's home page and click on the Projects > ENCODE menu item.