Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
- Christine Roden1,2,3,4,9,
- Jonathan Gaillard2,5,9,
- Shaveta Kanoria6,
- William Rennie6,
- Syndi Barish4,
- Jijun Cheng1,2,3,
- Wen Pan1,2,3,
- Jun Liu1,2,3,
- Chris Cotsapas1,7,
- Ye Ding6 and
- Jun Lu1,2,3,8
- 1Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
- 2Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA;
- 3Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA;
- 4Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA;
- 5School of Medicine, Yale University, New Haven, Connecticut 06510, USA;
- 6Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA;
- 7Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06511, USA;
- 8Yale Cooperative Center of Excellence in Hematology, Yale University, New Haven, Connecticut 06520, USA
- Corresponding author: jun.lu{at}yale.edu
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↵9 These authors contributed equally to this work.
Abstract
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing. We identify two bulge-depleted regions on the miRNA stem, located ∼16–21 nt and ∼28–32 nt from the base of the stem, that are less tolerant of unpaired bases. We further show that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. We predict that a small but significant fraction of human single-nucleotide polymorphisms (SNPs) alter pri-miRNA processing, and confirm several predictions experimentally including a disease-causing mutation. Our study enhances the rules governing mammalian pri-miRNA processing and suggests a diverse impact of human genetic variation on miRNA biogenesis.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.208900.116.
- Received April 25, 2016.
- Accepted January 6, 2017.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
