News: Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
3
gravatar for Chirag Nepal
2.8 years ago by
Chirag Nepal2.1k
Copenhagen
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

http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1354.full

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.          http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1354/F5.expansion.html  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. http://www.ncbi.nlm.nih.gov/pubmed/24002785 Processed data can be directly viewed on UCSC genome browser http://promshift.genereg.net/zebrafish/

 

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

http://nar.oxfordjournals.org/content/early/2015/12/15/nar.gkv1354/F4.expansion.html

 

cheers

Chirag

 

 

 

 

 

 

 

ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by Chirag Nepal2.1k
2

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by geek_y8.7k

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

ADD REPLYlink written 2.7 years ago by Chirag Nepal2.1k
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