ncRNA Vs miRNA

Question

[The Last Word]

What is the difference between non-coding RNAs and microRNAs. A protocol that I am following for predicting the miRNAs in a genome has a step in it where ncRNAs are filtered but I isn't miRNAs non coding RNAs in the first place? So why is this filter being implemented.

Reference

http://www.sciencedirect.com/science/article/pii/S0888754311001315

Answer 1

[David Fredman]

miRNAs are indeed small non-coding RNAs. We can detect them by sequencing all RNAs in a given size range, map them to the corresponding genome, and look for the places where reads stack up in a pattern indicating that it's a miRNA precursor (basically: two stacks of reads with a given spacing, precise drop-off in read coverage that indicates precise Dicer processing, the resulting sequence folds into a stable hairpin)

That pattern may, however, also be found at sites generating other types of small structural RNAs, e.g. tRNAs. Removing all sites/sequences known to generating other types of structural RNAs is an efficient heuristic that will remove a lot of "false positives" that we would otherwise have to identify as "non-miRNAs" by close inspection of the data, or might miss altogether.

In a recent study where we detected miRNAs in a non-model organism (but with a sequenced genome), we did it as follows:

Abundant noncoding RNAs (rRNAs, tRNAs, snRNAs, and snoRNAs) were annotated to the N. vectensis genome using BLASTN (version 2.2.18) to identify homologs of

1. Drosophila melanogaster annotated rRNAs, tRNAs, snRNAs, and snoRNAs (downloaded from FlyBase and GenBank),
2. the most abundant rRNA variants found in previous studies involving sequencing of small RNAs (Ghildiyal et al. 2008; Seitz et al. 2008),
3. Homo sapiens rRNAs, snRNAs, and snoRNAs (downloaded from GenBank, and the LBME human snoRNA database), and
4. the complete set of tRNAs found in the Genomic tRNA database.

Genomic sequences with a significant BLAST hit (E-value < 10^-4) to any of those databases were flagged as "abundant noncoding RNAs," and deep-sequencing reads showing perfect identity to one of those were discarded.

[The Last Word]

excellent and well researched answer

Answer 2

[Floris Brenk]

MicroRNAs are a type of non-coding RNAs. Other types of ncRNA are for example snoRNAs, siRNAs, snRNAs, exRNAs, and piRNAs and long ncRNAs. I guess that the filtering steps would be based on size or sequence motif.

[The Last Word]

How do you suggest that I weed out miRNA from the rest of the non-coding RNAs. The paper which I have linked says that it was done with Blastn but I just cant understand how that would suffice.

[Floris Brenk]

They probably blast all the obtained sequences and when they are already known in the database they remove them I guess.