title: The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes.
abstract: MicroRNAs (miRNAs) are small regulatory RNAs processed from stem-loop regions of primary transcripts (pri-miRNAs), with the choice of stem loops for initial processing largely determining what becomes a miRNA. To identify sequence and structural features influencing this choice, we determined cleavage efficiencies of >50,000 variants of three human pri-miRNAs, focusing on the regions intractable to previous high-throughput analyses. Our analyses revealed a mismatched motif in the basal stem region, a preference for maintaining or improving base pairing throughout the remainder of the stem, and a narrow stem-length preference of 35 ± 1 base pairs. Incorporating these features with previously identified features, including three primary-sequence motifs, yielded a unifying model defining mammalian pri-miRNAs in which motifs help orient processing and increase efficiency, with the presence of more motifs compensating for structural defects. This model enables generation of artificial pri-miRNAs, designed de novo, without reference to any natural sequence yet processed more efficiently than natural pri-miRNAs.
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Fang
authors.affiliation: Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: dbartel@wi.mit.edu.
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
mesh_terms: D019295:Computational Biology / Q000379:methods*; D053487:DEAD-box RNA Helicases / Q000378:metabolism; D057809:HEK293 Cells; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D043244:Ribonuclease III / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; C408087:DICER1 protein, human; C517918:DROSHA protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases