title: pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.
abstract: Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding these RNA before sequencing through locked nucleic acids (LNA), greatly increasing pre-miRNA sequence counts with no discernable effect on pre-miRNA or mature miRNA sequencing. Analysis of profiles generated in total, nuclear and cytoplasmic cell fractions reveals that pre-miRNAs are subject to a wide range of regulatory processes involving loci-specific 3'- and 5'-end variation entailing complex cleavage patterns with co-occurring polyuridylation. Additionally, examination of nuclear-enriched flanking sequences of pre-miRNA, particularly those derived from polycistronic miRNA transcripts, provides insight into miRNA and miRNA-offset (moRNA) production, specifically identifying novel classes of RNA potentially functioning as moRNA precursors. Our findings point to particularly intricate regulation of the let-7 family in many ways reminiscent of DICER1-independent, pre-mir-451-like processing, introduce novel and unify known forms of pre-miRNA regulation and processing, and shed new light on overlooked products of miRNA processing pathways.
authors: Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan. burrough@gsc.riken.jp
authors: A Maxwell
authors: AM
authors: Burroughs
authors: Mitsuoki
authors: M
authors: Kawano
authors: Yoshinari
authors: Y
authors: Ando
authors: Carsten O
authors: CO
authors: Daub
authors: Yoshihide
authors: Y
authors: Hayashizaki
mesh_terms: D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism; D059372:Nucleotide Motifs; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry*; D011072:Poly U / Q000032:analysis*; D012322:RNA Precursors / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D016601:RNA-Binding Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014529:Uridine / Q000032:analysis / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D009838:Oligodeoxyribonucleotides; D009841:Oligonucleotides; D012322:RNA Precursors; D016601:RNA-Binding Proteins; C477371:locked nucleic acid; D011072:Poly U; D014529:Uridine