title: Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis.
abstract: Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Export in 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells, whereas we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3' end, yielding miRNAs from the 5' strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.
authors.affiliation: Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Korea; Department of Biochemistry, Chonnam National University Medical School, Gwangju 61469, Korea; Center for Creative Biomedical Scientists, Chonnam National University Medical School, Gwangju 61469, Korea; narrykim@snu.ac.kr ykk@jnu.ac.kr.
authors.forename: Young-Kook
authors.initials: YK
authors.lastname: Kim
authors.affiliation: Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
authors.forename: Boseon
authors.initials: B
authors.lastname: Kim
authors.affiliation: Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea narrykim@snu.ac.kr ykk@jnu.ac.kr.
authors.forename: V Narry
authors.initials: VN
authors.lastname: Kim
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D055786:Gene Knockout Techniques; D006801:Humans; D028884:Karyopherins / Q000235:genetics / Q000378:metabolism*; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism*
chemical_list: D028884:Karyopherins; C572386:MIRN484 microRNA, human; D035683:MicroRNAs; C446511:XPO5 protein, human; C408087:DICER1 protein, human; C517918:DROSHA protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases
keywords: DICER; DROSHA; Exportin 5; knockout; microRNA