The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction

Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James J.; Hermida, Leandro; Primig, Michael

doi:10.1093/nar/gkl957

Cited by 19 publications

(24 citation statements)

References 25 publications

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“…Genomewide normalized and log2-transformed expression data at the single oligonucleotide probe level are accessible via GermOnline's Saccharomyces Genomics Viewer (www.germonline.org) (21).…”

Section: Resultsmentioning

confidence: 99%

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois

Liu

Walther

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

217

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Budding yeast noncoding RNAs (ncRNAs) are pervasively transcribed during mitosis, and some regulate mitotic protein-coding genes. However, little is known about ncRNA expression during meiotic development. Using high-resolution profiling we identified an extensive meiotic ncRNA expression program interlaced with the protein-coding transcriptome via sense/antisense transcript pairs, bidirectional promoters, and ncRNAs that overlap the regulatory regions of genes. Meiotic unannotated transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs and other ncRNAs accumulate in successive waves. Diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development. The present study demonstrates a unique function for budding yeast Rrp6 in degrading distinct classes of meiotically induced ncRNAs during vegetative growth and the onset of meiosis and thus points to a critical role of differential ncRNA expression in the execution of a conserved developmental program.

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Section: Resultsmentioning

confidence: 99%

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois

Liu

Walther

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

217

View full text Add to dashboard Cite

show abstract

“…Furthermore, links to facilitate information retrieval from external sources have been added. This includes the display of recently published articles from the Google Scholar service, and the display of community annotation entries from GermOnline [31,32]. …”

Section: Utility and Discussionmentioning

confidence: 99%

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists

et al. 2007

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“…E-TABM-531 corresponds to 12 duplicate samples collected at 0, 6 and 18 dpp from C57BL/6 control and Sox8/Sox9 mutant mice respectively. Normalized data for all loci represented on the GeneChip are available for viewing at www.germonline.org/ (Gattiker et al, 2007).…”

Section: Minimum Information About a Microarray Experiments Compliancementioning

confidence: 99%

Genome‐wide identification of Sox8‐, and Sox9‐dependent genes during early post‐natal testis development in the mouse

et al. 2013

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Genome-wide identification of Sox8-, and Sox9-dependent genes during early post-natal testis development in the mouse F. Chalmel,*,a A. Lardenois,*,a I. Georg, †, ‡,k F. Barrionuevo, †,** P. Demougin, § B. J egou,*, ¶ G. Scherer † and M. Primig* *Inserm, U1085-Irset, University of Rennes 1, Rennes, France, †Institute of Human Genetics, University of Freiburg, Freiburg, Germany, ‡Faculty for Biology, University of Freiburg, Freiburg, Germany, §Biozentrum, University of Basel, Basel, Switzerland, ¶EHESP School of Public Health (Rennes, Paris), Rennes Cedex, France, k Present address: Area of Human DNA Variability, Centro de Genomica e Investigacio Oncologica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucia, Granada, Spain, and **Departamento de Genetica e Instituto de Biotecnologia, Universidad de Granada, Armilla, Spain SUMMARYThe SOX8 and SOX9 transcription factors are involved in, among others, sex differentiation, male gonad development and adult maintenance of spermatogenesis. Sox8 À/À mice lacking Sox9 in Sertoli cells fail to form testis cords and cannot establish spermatogenesis. Although genetic and histological data show an important role for these transcription factors in regulating spermatogenesis, it is not clear which genes depend upon them at a genome-wide level. To identify transcripts that respond to the absence of Sox8 in all cells and Sox9 in Sertoli cells we measured mRNA concentrations in testicular samples from mice at 0, 6 and 18 days post-partum. In total, 621 and 629 transcripts were found at decreased or increased levels, respectively, at different time points in the mutant as compared to the control samples. These mRNAs were categorized as preferentially expressed in Sertoli cells or germ cells using data obtained with male and female gonad samples and enriched testicular cell populations. Five candidate genes were validated at the protein level. Furthermore, we identified putative direct SOX8 and SOX9 target genes by integrating predicted SOX-binding sites present in potential regulatory regions upstream of the transcription start site. Finally, we used protein network data to gain insight into the effects on regulatory interactions that occur when Sox8 and Sox9 are absent in developing Sertoli cells. The integration of testicular samples with enriched Sertoli cells, germ cells and female gonads enabled us to broadly distinguish transcripts directly affected in Sertoli cells from others that respond to secondary events in testicular cell types. Thus, combined RNA profiling signals, motif predictions and network data identified putative SOX8/SOX9 target genes in Sertoli cells and yielded insight into regulatory interactions that depend upon these transcription factors. In addition, our results will facilitate the interpretation of genome-wide in vivo SOX8 and SOX9 DNA binding data.

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The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction

Cited by 19 publications

References 25 publications

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists

Genome‐wide identification of Sox8‐, and Sox9‐dependent genes during early post‐natal testis development in the mouse

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