title: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation.
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.
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.|Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Roden
authors.affiliation: Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|School of Medicine, Yale University, New Haven, Connecticut 06510, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Gaillard
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA.
authors.forename: Shaveta
authors.initials: S
authors.lastname: Kanoria
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA.
authors.forename: William
authors.initials: W
authors.lastname: Rennie
authors.affiliation: Graduate Program in Biological and Biomedical Sciences, Yale University, New Haven, Connecticut 06510, USA.
authors.forename: Syndi
authors.initials: S
authors.lastname: Barish
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.
authors.forename: Jijun
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.
authors.forename: Wen
authors.initials: W
authors.lastname: Pan
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Department of Neurology, Yale School of Medicine, New Haven, Connecticut 06511, USA.
authors.forename: Chris
authors.initials: C
authors.lastname: Cotsapas
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA.
authors.forename: Ye
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA.|Yale Stem Cell Center and Yale Cancer Center, Yale University, New Haven, Connecticut 06520, USA.|Yale Center for RNA Science and Medicine, New Haven, Connecticut 06520, USA.|Yale Cooperative Center of Excellence in Hematology, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Lu
mesh_terms: D000818:Animals; D002460:Cell Line; D006801:Humans; D055029:Inverted Repeat Sequences; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012323:RNA Processing, Post-Transcriptional
chemical_list: D035683:MicroRNAs