Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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-coding 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 the rat using Illumina next-generation sequencing technology and highly enriched testicular cell populations. Among 20,424 high-confidence transcripts reconstructed, we defined a stringent set of 1,419 long multi-exonic unannotated transcripts expressed in the testis, named TUTs. These were classified into seven groups with different expression patterns. The vast majority of TUTs share many of the characteristics of vertebrate long non-coding 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 non-coding 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 of novel loci expressed during spermatogenesis that significantly contributes to the rat genome annotation. A graphical display of the data is conveniently accessible through the ReproGenomics Viewer (RGV) at http://rgv.genouest.org. Genome-wide expression profiling analysis using Illumina next-generation sequencing technology

ORGANISM(S): Rattus norvegicus

SUBMITTER: FrÃ©dÃ©ric Chalmel

PROVIDER: E-GEOD-48321 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-resolution profiling of novel transcribed regions during rat spermatogenesis.

Chalmel Frédéric F Lardenois Aurélie A Evrard Bertrand B Rolland Antoine D AD Sallou Olivier O Dumargne Marie-Charlotte MC Coiffec Isabelle I Collin Olivier O Primig Michael M Jégou Bernard B

Biology of reproduction 20140416 1

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 exp ...[more]

PMID: 24740603

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Project description:The early stages of the immune response against aberrant tissues such a tumors are technically difficult to study and therefore little understood. To analyze the innate immune response towards modified self-tissue we expressed a dominant-active version of the Ras oncogene in Drosophila imaginal discs and salivary glands. Signs of an immune response are observed on wings of adult flies, which show spots of melanization and in larvae, where the salivary glands attract blood cells. In line with the strong response mounted against salivary glands, they are found to express metalloproteases and apoptotic markers making them both accessible and recognizable for the immune system. The response against the glands bears several hallmarks of an encapsulation response including flattening of plasmatocytes, differentiation of lamellocytes, attachment of crystal cells and melanization at the final stage. RNA sequencing of the fat body, the primary producer of immune effectors, reveals a pattern of induced genes, which overlaps the one previously found upon wasp infestation but shows also several specific features. Evidence for the functional importance of one of the induced genes is presented proving the power of our approach to identify regulators of the response against modified self. Transcriptome analysis of the immune response in the fat body after expression of dominant-active RAS in the wing imaginal discs and salivary glands. Comparison of fat bodies from 3 control and 3 RAS-expressing larvae. For each sample fat bodies from 40 individuals were dissected. Differential gene expression files [output of Cuffdiff] are linked below: ResultsContr123vsRas123Individual.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to individual Ras induced; replicate analysis using Cuffdiff. ResultsContr123vsRas123Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to three Ras induced; replicate analysis using Cuffdiff. ResultsContr123vsRas12Multiple.xls: Output file of Cuffdiff. Differential gene expression analysis, three control compared to two Ras induced; replicate analysis using Cuffdiff.

Dataset Information

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis

Publications

High-resolution profiling of novel transcribed regions during rat spermatogenesis.

Similar Datasets

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