Since we launched EpiGenie, we’ve always considered ourselves big promoters of miRNA. Sure, we cover the big headers in chromatin and DNA methylation too, but it’s hard not to identify with these small, overlooked contributors… (OK enough with our high school sports sob stories). Once again we’ve been humbled by Mother Nature as a novel class of miRNA promoters has risen from the ranks, and they appear to be completely dedicated to miRNAs. Guess we’re going to have to step up our game.
Previously thought of as overhead in the regulatory office space, miRNAs have become more of the boss’ pet recently for their attention to detail and uncanny ability to sift through large amounts of code for small snippet, seed regions.
Since their discovery, the research community has assumed that, in most cases, miRNAs are transcribed from Pol II promoters intergenically, in some distant UTR, or intragenically, by piggybacking on the transcription of larger protein-coding transcripts. A talented team of researchers from the University of Pittsburgh just published data late last week showing that miRNA transcriptional regulation might not be that simple.
Unlike the field of mRNA transcriptional regulation, miRNA transcriptional regulation has been a relatively under-investigated area. Pitt’s Corcoran and colleagues decided that it was time to peer inside the black box of miRNA regulatory motifs, and take a crack at learning more about this critical mechanism.
In their recent work, they outline a new method for mapping miRNA transcriptional start sites (TSS) and promoters, and let us in on some of the surprises they found lurking upstream of miRNA coding regions. After all of the mapping and data sifting, they confirmed some previous findings as well as some surprising results that show:
- Inter and Intragenic miRNA transcripts are transcribed by Pol II promoters from as far as 40Kb from the pre-miR…how’s that for a long distance relationship??
- pri-miR transcripts can be tens of thousands of bases long, way longer than previously thought.?
- 26% of intragenic miRNAs are transcribed by their own unique promoters.?
- Most of these intragenic miRNA promoters had no CpG islands?
Join the Hunt
So what do you get for the researcher that has a mean thirst for miRNA promoter/TSS investigations? Custom tiling arrays in this case. The team from Pitt assaulted these unsuspecting regulatory regions with chromatin immunoprecipitation (ChIP) combo’d with 44K custom arrays from Agilent’s eArray offering. This particular custom array goes by the name of AMADID 014119 and though it may sound like a prisoner’s ID number, the 100 Kb tiled regions surrounding miRNA loci will be all but confining, enabling quick mapping and location analysis of Pol II enriched material.
This paper is packed with more details you won’t want to miss so check it out for yourself at PLoS One, April 2009
Want to learn more about Agilent’s custom arrays? Visit eArray.