RRC ID 69231
Author Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y.
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.
Journal Nucleic Acids Res
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.
Volume 40(4)
Pages 1424-37
Published 2012-2-1
DOI 10.1093/nar/gkr903
PII gkr903
PMID 22058130
PMC PMC3287202
MeSH HeLa Cells High-Throughput Nucleotide Sequencing Humans MicroRNAs / chemistry* MicroRNAs / metabolism Nucleotide Motifs Oligodeoxyribonucleotides / chemistry Oligonucleotides / chemistry* Poly U / analysis* RNA Precursors / chemistry* RNA Precursors / metabolism RNA Processing, Post-Transcriptional* RNA-Binding Proteins / metabolism Sequence Analysis, RNA Uridine / analysis Uridine / metabolism
IF 11.502
Resource
Human and Animal Cells HeLa(RCB0007)