Finding miRNA promoter in UCSC genome browser?

Question

[g-frans]

Hello. I'm having difficulties finding a promoter in the UCSC genome browser. The promoter is for the miRNA ENSG00000207926.1.

The miRNA is on the negative strand and is highly conserved (only the miRNA is highly conserved) My guess would be that it is a promoter, can someone help me? :)

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr3%3A52294114-52294413&hgsid=585693531_RdIVOtxdYX2DuqrKWFv1jtOWIhJL

Answer 1

[i.sudbery]

The primary transcripts for miRNAs are often not annotated - that is we often don't really know what they are. One reason for this is that they are unstable, and so unlikely to be picked up in cDNA/EST libraries. Other than the the mature miRNA, they are often not conserved either, so they can't be found that way.

The miRNA you link to is in the intron of the GLYCLT-AS1 transcript. miRNAs are often transcribed from introns (around 50% of human miRNAs are intronic). Looking at the "Layered H3K27ac" track, it would appear there is indeed some indications of regulator chromatin at the 5' end of the transcript, but not much elsewhere upstream of the the miRNA. Thus my first guess would be that this GLYCLT-AS1 is the microRNAs primary transcript, and that the patch of H3K27ac at the start of it represents the promoter. But really there is not way of knowing this for sure bioinformatically.

Answer 2

[g-frans]

Thank you for your answer. That helped!