3 replies to this topic

[MicroRNAQa]

Hi everyone.
I have a question regarding to microRNA promoter activity. I want to check luciferase for mmu-miR-124. The reason to check this to evaluate that my chemical or overexpression of gene (that chemical direct target) can induce promoter activity of this microRNA. I have real time and nothern blot data which shows that the treatment of the my chemical or overexpression of the gene induce the expression of mmu-miR-124. So could somebody suggest me how to find promoter sequence of that microRNA. and how I can proceed further for tha above purpose.
if you have some alternative of this experiment then please also let me know.
Thank you in anticipating

[mike.sh]

Check out miRGen2.0 database containing predicted TSS regions and TFBSs in miRNA promoters. In the corresponding paper there are references to some works on promoter prediction that authors used to build the database. Hope this helps.
PS To identify if your chemical's target gene binds to the promoter you can try ChIP and also do some TFBS search (in case if your gene is a known transcription factor) in the promoter region.

Edited by mike.sh, 03 July 2011 - 03:58 AM.

[pcrman]

Is the miRNA independently transcribed or in the intron of another gene? For the latter, it may not have its own promoter, for the former, you can just assume the sequence upstream of the start of the primary miRNA is the promoter. You can use that sequence to predict how likely it is a promoter. In general, miRNA promoters are not well characterized, and more obscure than protein coding genes.

[whitedolphin]

MicroRNAQa, on 28 June 2011 - 06:46 PM, said:

Hi everyone.
I have a question regarding to microRNA promoter activity. I want to check luciferase for mmu-miR-124. The reason to check this to evaluate that my chemical or overexpression of gene (that chemical direct target) can induce promoter activity of this microRNA. I have real time and nothern blot data which shows that the treatment of the my chemical or overexpression of the gene induce the expression of mmu-miR-124. So could somebody suggest me how to find promoter sequence of that microRNA. and how I can proceed further for tha above purpose.
if you have some alternative of this experiment then please also let me know.
Thank you in anticipating

pcrman, on 08 July 2011 - 08:49 PM, said:

Is the miRNA independently transcribed or in the intron of another gene? For the latter, it may not have its own promoter, for the former, you can just assume the sequence upstream of the start of the primary miRNA is the promoter. You can use that sequence to predict how likely it is a promoter. In general, miRNA promoters are not well characterized, and more obscure than protein coding genes.

I guess you may first identify pri-miR-124's TSS using RACE method, then characterize its promoter's sequence and activity combining bioinformatical prediction and ChIP experiment.