Rna-Seq: Distinguish Lncrna Of Smrna Precursors

Question

[int11ap1]

Hi everybody,

I have some data from RNA-seq. This data does NOT come from a library of small RNAs, but comes from a library of mRNAs and total RNA. From this data, I perform an alignment with TopHat, followed by cufflinks and annotation of the genes. After this point, I have a pipeline that extracts the lncRNAs from the other RNAs.

Once I have the lncRNAs, how could I differentiate the precursors of small RNAs from the "real" lncRNAs? I know that the vast majority of publications performs a BLAST against the database of miRNAs, and I have that in mind. However, I would like to ask if there exists another method, software, etc. that takes into account the secondary structure of the lncRNAs in order to say: OK, this might be a precursor of any small RNA (miRNA, siRNA, shRNA,...).

Do you have some suggestions?

Thanks in advance.

PD: I am working with plant transcriptome.

Answer 1

[Chirag Nepal]

Simple way is to overlap the coordinates of small RNAs and lncrna, and filter such lncrnas, as you mentioned. You can filter those precursor of well annotated. But my suggestion is, don't throw them out, have a look at it. Like thousands of protein coding genes, many lncrna also have small RNAs across their body, which might be generated during post-transcriptional activities or other unknown mechanisms. If you map small RNA data from same cell lines, you will see many of your lincrna have small RNAs along the transcripts.