title: Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing.
abstract: To use microRNAs to downregulate mRNA targets, cells must first process these ~22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants. Our results confirmed the importance of pairing in the stem and revealed three primary-sequence determinants, including an SRp20-binding motif (CNNC) found downstream of most pri-miRNA hairpins in bilaterian animals, but not in nematodes. Adding this and other determinants to C. elegans pri-miRNAs imparted efficient processing in human cells, thereby confirming the importance of primary-sequence determinants for distinguishing pri-miRNAs from other hairpin-containing transcripts.
authors: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors: Vincent C
authors: VC
authors: Auyeung
authors: Igor
authors: I
authors: Ulitsky
authors: Sean E
authors: SE
authors: McGeary
authors: David P
authors: DP
authors: Bartel
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D002457:Cell Extracts / Q000737:chemistry; D006801:Humans; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D046912:Multiprotein Complexes / Q000378:metabolism; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012323:RNA Processing, Post-Transcriptional; D016601:RNA-Binding Proteins / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism; D000068103:Serine-Arginine Splicing Factors
chemical_list: D002457:Cell Extracts; D035683:MicroRNAs; D046912:Multiprotein Complexes; D016601:RNA-Binding Proteins; C491388:SRSF3 protein, human; D000068103:Serine-Arginine Splicing Factors; D043244:Ribonuclease III