title: Microprocessor activity controls differential miRNA biogenesis In Vivo.
abstract: In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.
authors.affiliation: Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Conrad
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Mathematics and Informatics, Free University of Berlin, 14195 Berlin, Germany.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Marsico
authors.affiliation: Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biochemistry, Free University of Berlin, 14195 Berlin, Germany.
authors.forename: Maja
authors.initials: M
authors.lastname: Gehre
authors.affiliation: Otto Warburg Laboratories, Noncoding RNA Research Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. Electronic address: oerom@molgen.mpg.de.
authors.forename: Ulf Andersson
authors.initials: UA
authors.lastname: Orom
mesh_terms: D006367:HeLa Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D016601:RNA-Binding Proteins / Q000378:metabolism*; D043244:Ribonuclease III / Q000378:metabolism*; D059467:Transcriptome
chemical_list: C474043:DGCR8 protein, human; D035683:MicroRNAs; D016601:RNA-Binding Proteins; C517918:DROSHA protein, human; D043244:Ribonuclease III