title: piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells.
abstract: BACKGROUND
  Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3' UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis.
  
  
  RESULTS
  We identified 2710 piRNA clusters associated with 3' UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35% of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3'UTRs. Extended 3' UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3'UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs.
  
  
  CONCLUSIONS
  The finding that piRNAs are processed from extended 3' UTRs suggests a role for piRNAs in the remodeling of 3' UTRs. The presence of both clusters and extended 3'UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated.
authors.affiliation: Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA. yamtich@gmail.com.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Yamtich
authors.affiliation: Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA. sheo@chori.org.
authors.forename: Seok-Jin
authors.initials: SJ
authors.lastname: Heo
authors.affiliation: Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA. jdhahbi@chori.org.
authors.forename: Joseph
authors.initials: J
authors.lastname: Dhahbi
authors.affiliation: Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA. dimartin@chori.org.
authors.forename: David I K
authors.initials: DI
authors.lastname: Martin
authors.affiliation: Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA. dboffelli@chori.org.
authors.forename: Dario
authors.initials: D
authors.lastname: Boffelli
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics; D008297:Male; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D013737:Testis / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D060565:Argonaute Proteins; C546575:PIWIL4 protein, mouse; D012333:RNA, Messenger; D034741:RNA, Small Interfering