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. 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.