Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production.
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.
Pawlicki
Jan M
JM
Department of Pharmacology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
Steitz
Joan A
JA
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
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