title: Conserved and highly expressed tRNA derived fragments in zebrafish.
abstract: BACKGROUND
  Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire.
  
  
  RESULTS
  Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish. The tRFs identified are 18-30 nt long, are derived from specific 5' and 3' processing of mature tRNAs and are differentially expressed during development and in differentiated tissues, suggesting that they are likely produced by specific processing rather than random degradation of tRNAs. We further show that a highly expressed tRF (5'tRF-Pro(CGG)) is cleaved in vitro by Dicer and has silencing ability, indicating that it can enter the RNAi pathway. A computational analysis of zebrafish tRFs shows that they are conserved among vertebrates and mining of publicly available datasets reveals that some 5'tRFs are differentially expressed in disease conditions, namely during infection and colorectal cancer.
  
  
  CONCLUSIONS
  tRFs constitute a class of conserved regulatory RNAs in vertebrates and may be involved in mechanisms of genome regulation and in some diseases.
authors.affiliation: Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal. ana.r.soares@ua.pt.
authors.forename: Ana Raquel
authors.initials: AR
authors.lastname: Soares
authors.affiliation: Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal. noemia@ua.pt.
authors.forename: Noémia
authors.initials: N
authors.lastname: Fernandes
authors.affiliation: Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal. marisareverendo@ua.pt.
authors.forename: Marisa
authors.initials: M
authors.lastname: Reverendo
authors.affiliation: IEETA, University of Aveiro, 3810-193, Aveiro, Portugal. hugo.rafael@ua.pt.
authors.forename: Hugo Rafael
authors.initials: HR
authors.lastname: Araújo
authors.affiliation: IEETA, University of Aveiro, 3810-193, Aveiro, Portugal. jlo@ua.pt.
authors.forename: José Luís
authors.initials: JL
authors.lastname: Oliveira
authors.affiliation: Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal. gmoura@ua.pt.
authors.forename: Gabriela M R
authors.initials: GM
authors.lastname: Moura
authors.affiliation: Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal. msantos@ua.pt.
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D002460:Cell Line; D015179:Colorectal Neoplasms / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D041681:NIH 3T3 Cells; D034622:RNA Interference; D058727:RNA, Small Untranslated / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D043244:Ribonuclease III / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015027:Zebrafish
chemical_list: D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D012343:RNA, Transfer; D043244:Ribonuclease III