News: Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
gravatar for Chirag Nepal
2.6 years ago by
Chirag Nepal2.1k
Chirag Nepal2.1k wrote:

Hi all,

We have annotated the promoters of zebrafish miRNA primary (pri-miRNA) transcripts using CAGE-seq, histone ChIP-seq, RNAPII and RNA-seq. Annotated pri-miRNA promoters are good reference point for wet-lab people working on zebrafish miRNAs. We also validated seven paralogous copies of miR-9 pri-miRNAs by 5' RACE-PCR, in-situ and 3' RACE PCR. The paper is described here

We also showed that CAGE-seq detects Drosha processing events on active pre-miRNAs. This method is very useful to validate novel pre-miRNAs as it detects a distinct CAGE tag at the Drosha cleavage site.  For eg: If you want to validate some novel pre-miRNA in zebrafish, expressed during early embryogenesis, have a look at the zebrafish CAGE-seq data from the initial paper. Processed data can be directly viewed on UCSC genome browser


Additionally, we also showed that pre-miRNAs have enriched H3K4me3, H2A.Z, PolII peaks.











ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by Chirag Nepal2.1k

Very interesting. It would be good to if biostars has a Post type "papers" to discuss interesting papers in genomics.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by geek_y8.6k

Thanks !! It will be indeed nice to have a post type "Papers".

ADD REPLYlink written 2.6 years ago by Chirag Nepal2.1k
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