title: Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production.
abstract: MicroRNAs (miRNAs) are noncoding RNAs with important roles in regulating gene expression. In studying the earliest nuclear steps of miRNA biogenesis, we observe that primary miRNA (pri-miRNA) transcripts retained at transcription sites due to the deletion of 3'-end processing signals are converted more efficiently into precursor miRNAs (pre-miRNAs) than pri-miRNAs that are cleaved, polyadenylated, and released. Flanking exons, which also increase retention at transcription sites, likewise contribute to increased levels of intronic pri-miRNAs. Consistently, efficiently processed endogenous pri-miRNAs are enriched in chromatin-associated nuclear fractions. In contrast, pri-miRNAs that accumulate to high nuclear levels after cleavage and polyadenylation because of the presence of a viral RNA element (the ENE of the Kaposi's sarcoma-associated herpes virus polyadenylated nuclear RNA) are not efficiently processed to precursor or mature miRNAs. Exogenous pri-miRNAs unexpectedly localize to nuclear foci containing splicing factor SC35; yet these foci are unlikely to represent sites of miRNA transcription or processing. Together, our results suggest that pri-miRNA processing is enhanced by coupling to transcription.
authors.affiliation: Department of Pharmacology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
authors.forename: Jan M
authors.initials: JM
authors.lastname: Pawlicki
authors.forename: Joan A
authors.initials: JA
authors.lastname: Steitz
mesh_terms: D002843:Chromatin / Q000235:genetics; D005091:Exons / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D007438:Introns / Q000235:genetics; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics*; D009687:Nuclear Proteins / Q000378:metabolism; D026723:Polyadenylation; D012320:RNA Polymerase III / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D034443:RNA Transport; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012261:Ribonucleoproteins / Q000378:metabolism; D017384:Sequence Deletion; D000068103:Serine-Arginine Splicing Factors; D013347:Subcellular Fractions; D014158:Transcription, Genetic; D039221:mRNA Cleavage and Polyadenylation Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D035683:MicroRNAs; D009687:Nuclear Proteins; D012333:RNA, Messenger; D012367:RNA, Viral; D012261:Ribonucleoproteins; D039221:mRNA Cleavage and Polyadenylation Factors; C073288:SRSF2 protein, human; D000068103:Serine-Arginine Splicing Factors; D012320:RNA Polymerase III