title: 5' isomiR variation is of functional and evolutionary importance.
abstract: We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK National University of Malaysia, Kuala Lumpur, Malaysia.
authors: Geok Chin
authors: GC
authors: Tan
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Elcie
authors: E
authors: Chan
authors: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
authors: Attila
authors: A
authors: Molnar
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Rupa
authors: R
authors: Sarkar
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Diana
authors: D
authors: Alexieva
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Ihsan Mad
authors: IM
authors: Isa
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Sophie
authors: S
authors: Robinson
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Shuchen
authors: S
authors: Zhang
authors: Wellcome Trust Genome Campus, Hinxton, CB10 S1A, UK.
authors: Peter
authors: P
authors: Ellis
authors: Wellcome Trust Genome Campus, Hinxton, CB10 S1A, UK.
authors: Cordelia F
authors: CF
authors: Langford
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Pascale V
authors: PV
authors: Guillot
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Anil
authors: A
authors: Chandrashekran
authors: University of Queensland Centre for Clinical Research, Brisbane, Australia.
authors: Nick M
authors: NM
authors: Fisk
authors: Imperial Centre for Translational and Experimental Medicine (ICTEM), Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Leandro
authors: L
authors: Castellano
authors: Max-Planck-Institut für Biochemi, Am Klopferspitz 1, D-82152 Martinsried, Germany University of Regensburg, Universitaetsstrasse, Germany.
authors: Gunter
authors: G
authors: Meister
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Robert M
authors: RM
authors: Winston
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK.
authors: Wei
authors: W
authors: Cui
authors: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
authors: David
authors: D
authors: Baulcombe
authors: Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK n.dibb@imperial.ac.uk.
authors: Nick J
authors: NJ
authors: Dibb
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000378:metabolism; D002460:Cell Line; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000737:chemistry; D012333:RNA, Messenger / Q000378:metabolism; D013234:Stem Cells / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D012322:RNA Precursors; D012333:RNA, Messenger