title: High-resolution profiling of novel transcribed regions during rat spermatogenesis.
abstract: Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-encoding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in rat, using next-generation sequencing technology and highly enriched testicular cell populations. Among 20 424 high-confidence transcripts reconstructed, we defined a stringent set of 1419 long multi-exonic unannotated transcripts expressed in the testis (testis-expressed unannotated transcripts [TUTs]). TUTs were divided into 7 groups with different expression patterns. Most TUTs share many of the characteristics of vertebrate long noncoding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of noncoding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource for novel loci expressed during spermatogenesis that significantly contributes to rat genome annotation.
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France frederic.chalmel@inserm.fr.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Chalmel
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lardenois
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Evrard
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Antoine D
authors.initials: AD
authors.lastname: Rolland
authors.affiliation: Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA)-GenOuest platform, Rennes, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Sallou
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Marie-Charlotte
authors.initials: MC
authors.lastname: Dumargne
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Coiffec
authors.affiliation: Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA)-GenOuest platform, Rennes, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Collin
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
authors.affiliation: Inserm U1085-IRSET, Université de Rennes 1, Rennes, France Ecole des Hautes Études en Santé Publique, Rennes, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Jégou
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D017207:Rats, Sprague-Dawley; D013091:Spermatogenesis / Q000235:genetics*; D013094:Spermatozoa / Q000166:cytology* / Q000378:metabolism; D013737:Testis / Q000166:cytology* / Q000378:metabolism; D014158:Transcription, Genetic
keywords: RNA profiling; Sertoli cells; intergenic transcripts; intronic transcripts; lncRNAs; mammalian spermatogenesis; novel transcribed regions