title: XenopusPiwi proteins interact with a broad proportion of the oocyte transcriptome.
abstract: Piwi proteins utilize small RNAs (piRNAs) to recognize target transcripts such as transposable elements (TE). However, extensive piRNA sequence diversity also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To determine Piwi target RNAs, we used ribonucleoprotein-immunoprecipitation (RIP) and cross-linking and immunoprecipitation (CLIP) to identify thousands of transcripts associated with the Piwi proteins XIWI and XILI (Piwi-protein-associated transcripts, PATs) from early stage oocytes ofX. laevisandX. tropicalisMost PATs associate with both XIWI and XILI and include transcripts of developmentally important proteins in oogenesis and embryogenesis. Only a minor fraction of PATs in both frog species displayed near perfect matches to piRNAs. Since predicting imperfect pairing between all piRNAs and target RNAs remains intractable, we instead determined that PAT read counts correlate well with the lengths and expression levels of transcripts, features that have also been observed for oocyte mRNAs associated withDrosophilaPiwi proteins. We used an in vitro assay with exogenous RNA to confirm that XIWI associates with RNAs in a length- and concentration-dependent manner. In this assay, noncoding transcripts with many perfectly matched antisense piRNAs were unstable, whereas coding transcripts with matching piRNAs were stable, consistent with emerging evidence that Piwi proteins both promote the turnover of TEs and other RNAs, and may also regulate mRNA localization and translation. Our study suggests that Piwi proteins play multiple roles in germ cells and establishes a tractable vertebrate system to study the role of Piwi proteins in transcript regulation.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Toombs
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Yuliya A
authors.initials: YA
authors.lastname: Sytnikova
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Gung-Wei
authors.initials: GW
authors.lastname: Chirn
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Ignatius
authors.initials: I
authors.lastname: Ang
authors.affiliation: Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: Nelson C
authors.identifier: 0000-0001-9907-1404
authors.initials: NC
authors.lastname: Lau
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Michael D
authors.identifier: 0000-0002-5037-1972
authors.initials: MD
authors.lastname: Blower
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D001681:Biological Assay; D004251:DNA Transposable Elements; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D018507:Gene Expression Regulation, Developmental; D009865:Oocytes / Q000254:growth & development / Q000378:metabolism*; D009866:Oogenesis / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome; D014981:Xenopus / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029867:Xenopus Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D029721:Drosophila Proteins; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D029867:Xenopus Proteins; C116498:piwi protein, Drosophila
keywords: Piwi; XILI; XIWI; Xenopus; oocyte