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Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data

Corcoran, DL and Pandit, KV and Gordon, B and Bhattacharjee, A and Kaminski, N and Benos, PV (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS ONE, 4 (4).

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Abstract

Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology: We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion: miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex. © 2009 Corcoran et al.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Corcoran, DL
Pandit, KV
Gordon, B
Bhattacharjee, A
Kaminski, N
Benos, PVbenos@pitt.eduBENOS
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorPatil, Christopher K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 23 April 2009
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 4
Number: 4
DOI or Unique Handle: 10.1371/journal.pone.0005279
Schools and Programs: Graduate School of Public Health > Human Genetics
School of Medicine > Biomedical Informatics
School of Medicine > Computational Biology
School of Medicine > Critical Care Medicine
Refereed: Yes
PubMed Central ID: PMC2668758
PubMed ID: 19390574
Date Deposited: 25 Jul 2012 14:19
Last Modified: 02 Feb 2019 16:56
URI: http://d-scholarship.pitt.edu/id/eprint/13126

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