Nelson P.J.,Ludwig Maximilians University of Munich |
Werner T.,Genomatix Software GmbH |
Werner T.,University of Michigan
Seminars in Nephrology | Year: 2010
Systems-level approaches provide help in characterizing the complexity of renal disease. In this review, we illustrate, using a series of recent examples of integrative studies based on pathway analysis and promoter networks, how new techniques allow the analysis of the layout of complex systems and, through this, help answer questions related to renal disease processes. These technologies include the identification of regulatory pathways dysregulated in the context of renal disease, and techniques for studying promoter networks. Both approaches make use of technologies applied to large-scale transcriptomics, transcriptomic profiling by DNA microarrays, or next-generation sequencing. © 2010 Elsevier Inc.
Fiesel F.C.,Hertie Institute for Clinical Brain Research |
Weber S.S.,Hertie Institute for Clinical Brain Research |
Supper J.,University of Tubingen |
Supper J.,Genomatix Software GmbH |
And 2 more authors.
Nucleic Acids Research | Year: 2012
TDP-43 is linked to neurodegenerative diseases including frontotemporal dementia and amyotrophic lateral sclerosis. Mostly localized in the nucleus, TDP-43 acts in conjunction with other ribonucleoproteins as a splicing co-factor. Several RNA targets of TDP-43 have been identified so far, but its role(s) in pathogenesis remains unclear. Using Affymetrix exon arrays, we have screened for the first time for splicing events upon TDP-43 knockdown. We found alternative splicing of the ribosomal S6 kinase 1 (S6K1) Aly/REF-like target (SKAR) upon TDP-43 knockdown in non-neuronal and neuronal cell lines. Alternative SKAR splicing depended on the first RNA recognition motif (RRM1) of TDP-43 and on 5′-GA-3' and 5′-UG-3′ repeats within the SKAR pre-mRNA. SKAR is a component of the exon junction complex, which recruits S6K1, thereby facilitating the pioneer round of translation and promoting cell growth. Indeed, we found that expression of the alternatively spliced SKAR enhanced S6K1-dependent signaling pathways and the translational yield of a splice-dependent reporter. Consistent with this, TDP-43 knockdown also increased translational yield and significantly increased cell size. This indicates a novel mechanism of deregulated translational control upon TDP-43 deficiency, which might contribute to pathogenesis of the protein aggregation diseases frontotemporal dementia and amyotrophic lateral sclerosis. © 2011 The Author(s).
Werner T.,Genomatix Software GmbH
Briefings in Bioinformatics | Year: 2010
Genome-wide sequencing has enabled modern biomedical research to relate more and more events in healthy as well as disease-affected cells and tissues to the genomic sequence. Now next generation sequencing (NGS) extends that reach into multiple almost complete genomes of the same species, revealing more and more details about how individual genomes as well as individual aspects of their regulation differ from each other. The inclusion of NGS-based transcriptome sequencing, chromatin-immunoprecipitation (ChIP) of transcription factor binding and epigenetic analyses (usually based on DNA methylation or histone modification ChIP) completes the picture with unprecedented resolution enabling the detection of even subtle differences such as alternative splicing of individual exons. Functional genomics aims at the elucidation of the molecular basis of biological functions and requires analyses that go far beyond the primary analysis of the reads such as mapping to a genome template sequence. The various and complex interactions between the genome, gene products and metabolites define biological function, which necessitates inclusion of results other than sequence tags in quite elaborative approaches. However, the extra efforts pay off in revealing mechanisms as well as providing the foundation for new strategies in systems biology and personalized medicine. This review emphasizes the particular contribution NGS-based technologies make to functional genomics research with a special focus on gene regulation by transcription factor binding sites. © The Author 2010. Published by Oxford University Press.
Supper J.,Genomatix Software GmbH
Methods (San Diego, Calif.) | Year: 2013
In recent years, gene fusions have gained significant recognition as biomarkers. They can assist treatment decisions, are seldom found in normal tissue and are detectable through Next-generation sequencing (NGS) of the transcriptome (RNA-seq). To transform the data provided by the sequencer into robust gene fusion detection several analysis steps are needed. Usually the first step is to map the sequenced transcript fragments (RNA-seq) to a reference genome. One standard application of this approach is to estimate expression and detect variants within known genes, e.g. SNPs and indels. In case of gene fusions, however, completely novel gene structures have to be detected. Here, we describe the detection of such gene fusion events based on our comprehensive transcript annotation (ElDorado). To demonstrate the utility of our approach, we extract gene fusion candidates from eight breast cancer cell lines, which we compare to experimentally verified gene fusions. We discuss several gene fusion events, like BCAS3-BCAS4 that was only detected in the breast cancer cell line MCF7. As supporting evidence we show that gene fusions occur more frequently in copy number enriched regions (CNV analysis). In addition, we present the Transcriptome Viewer (TViewer) a tool that allows to interactively visualize gene fusions. Finally, we support detected gene fusions through literature mining based annotations and network analyses. In conclusion, we present a platform that allows detecting gene fusions and supporting them through literature knowledge as well as rich visualization capabilities. This enables scientists to better understand molecular processes, biological functions and disease associations, which will ultimately lead to better biomedical knowledge for the development of biomarkers for diagnostics and therapies. Copyright © 2012 Elsevier Inc. All rights reserved.
Werner T.,Genomatix Software GmbH |
Werner T.,University of Michigan
Reproduction, Fertility and Development | Year: 2011
Reproduction and fertility are controlled by specific events naturally linked to oocytes, testes and early embryonal tissues. A significant part of these events involves gene expression, especially transcriptional control and alternative transcription (alternative promoters and alternative splicing). While methods to analyse such events for carefully predetermined target genes are well established, until recently no methodology existed to extend such analyses into a genome-wide de novo discovery process. With the arrival of next generation sequencing (NGS) it becomes possible to attempt genome-wide discovery in genomic sequences as well as whole transcriptomes at a single nucleotide level. This does not only allow identification of the primary changes (e.g. alternative transcripts) but also helps to elucidate the regulatory context that leads to the induction of transcriptional changes. This review discusses the basics of the new technological and scientific concepts arising from NGS, prominent differences from microarray-based approaches and several aspects of its application to reproduction and fertility research. These concepts will then be illustrated in an application example of NGS sequencing data analysis involving postimplantation endometrium tissue from cows. © 2011 IETS.