title: Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate.
abstract: Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here, we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis was piRNAs, although 353 novel miRNAs but few endo-siRNAs were also identified. MARWI, a marmoset homolog of mouse MIWI and a very abundant PIWI in adult testes, associates with piRNAs that show characteristics of mouse pachytene piRNAs. As in other mammals, most marmoset piRNAs are derived from conserved clustered regions in the genome, which are annotated as intergenic regions. However, unlike in mice, marmoset piRNA clusters are also found on the X chromosome, suggesting escape from meiotic sex chromosome inactivation by the X-linked clusters. Some of the piRNA clusters identified contain antisense-orientated pseudogenes, suggesting the possibility that pseudogene-derived piRNAs may regulate parental functional protein-coding genes. More piRNAs map to transposable element (TE) subfamilies when they have copies in piRNA clusters. In addition, the strand bias observed for piRNAs mapped to each TE subfamily correlates with the polarity of copies inserted in clusters. These findings suggest that pachytene piRNA clusters determine the abundance and strand-bias of TE-derived piRNAs, may regulate protein-coding genes via pseudogene-derived piRNAs, and may even play roles in meiosis in the adult marmoset testis.
authors.affiliation: Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Takamasa
authors.initials: T
authors.lastname: Hirano
authors.affiliation: Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Yuka W
authors.initials: YW
authors.lastname: Iwasaki
authors.affiliation: Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Zachary Yu-Ching
authors.initials: ZY
authors.lastname: Lin
authors.affiliation: Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan.
authors.forename: Masanori
authors.initials: M
authors.lastname: Imamura
authors.affiliation: Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Naomi M
authors.initials: NM
authors.lastname: Seki
authors.affiliation: Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan Central Institute for Experimental Animals, Kawasaki, Kanagawa 210-0821, Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Sasaki
authors.affiliation: Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Kuniaki
authors.initials: K
authors.lastname: Saito
authors.affiliation: Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Okano
authors.affiliation: Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
authors.forename: Mikiko C
authors.initials: MC
authors.lastname: Siomi
authors.affiliation: Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Siomi
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D002144:Callithrix / Q000235:genetics*; D004251:DNA Transposable Elements; D015870:Gene Expression; D020869:Gene Expression Profiling; D016678:Genome; D008297:Male; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D020161:Physical Chromosome Mapping; D011485:Protein Binding; D011544:Pseudogenes; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D013737:Testis / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D034741:RNA, Small Interfering; D012343:RNA, Transfer
keywords: PIWI; miRNAs; piRNAs; pseudogenes; transposable elements