title: Knockout of miR-221 and miR-222 reveals common and specific targets for paralogous miRNAs.
abstract: MicroRNAs (miRNAs) regulate the expression of mRNA through sequence-specific binding of the 3' untranslated region (UTR). The seed sequence of miRNAs is the key determinant for target site recognition. Paralogous miRNAs, which share the same seed sequences but differ in their 3' regions, are known to regulate largely overlapping groups of mRNAs. However, no study has analyzed functional differences between paralogous miRNAs with proper experimental methods. In this study, we compared the targets of paralogous miRNAs, miR-221 and miR-222. Using a nuclease-mediated genome engineering technique, we established knockout cell lines for these miRNAs, and precisely analyzed differences in target regulation. We found that miR-221 and miR-222 suppress the previously identified targets, CDKN1B and CDKN1C, differentially. Whereas both miRNAs suppressed CDKN1B, only miR-221 suppressed CDKN1C. From transcriptome analyses, we found that several different target mRNAs were regulated by each of miR-221 and miR-222 independently, although a large number of mRNAs responded commonly to miR-221 and miR-222. This is the first study to compare the mRNA regulations by paralogous miRNAs and illustrate that paralogous miRNAs with the same seed sequence also have difference in target regulation.
authors.affiliation: a Department of Biochemistry , Chonnam National University Medical School , Gwangju , Korea.|b Center for Creative Biomedical Scientists, Chonnam National University Medical School , Gwangju , Korea.|c Basic Research Laboratory for Cardiac Remodeling, Chonnam National University Medical School , Gwangju , Korea.
authors.forename: Geon
authors.initials: G
authors.lastname: Jeong
authors.affiliation: a Department of Biochemistry , Chonnam National University Medical School , Gwangju , Korea.|b Center for Creative Biomedical Scientists, Chonnam National University Medical School , Gwangju , Korea.|c Basic Research Laboratory for Cardiac Remodeling, Chonnam National University Medical School , Gwangju , Korea.
authors.forename: Yeong-Hwan
authors.initials: YH
authors.lastname: Lim
authors.affiliation: a Department of Biochemistry , Chonnam National University Medical School , Gwangju , Korea.|b Center for Creative Biomedical Scientists, Chonnam National University Medical School , Gwangju , Korea.|c Basic Research Laboratory for Cardiac Remodeling, Chonnam National University Medical School , Gwangju , Korea.
authors.forename: Nam Joong
authors.initials: NJ
authors.lastname: Kim
authors.affiliation: d Daegu Gyeongbuk Medical Innovation Foundation , Daegu , Korea.
authors.forename: Gabbine
authors.initials: G
authors.lastname: Wee
authors.affiliation: a Department of Biochemistry , Chonnam National University Medical School , Gwangju , Korea.|b Center for Creative Biomedical Scientists, Chonnam National University Medical School , Gwangju , Korea.|c Basic Research Laboratory for Cardiac Remodeling, Chonnam National University Medical School , Gwangju , Korea.
authors.forename: Young-Kook
authors.initials: YK
authors.lastname: Kim
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D055786:Gene Knockout Techniques; D017930:Genes, Reporter; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D000069896:Transcription Activator-Like Effector Nucleases / Q000378:metabolism; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D000069896:Transcription Activator-Like Effector Nucleases; C525709:MIR221, human; C525710:MIR222, human
keywords: Knockout; TALEN; miR-221; miR-222; microRNA