Scientists generate gene expression atlas for mice
EU-funded scientists have generated a gene expression atlas for the developing mouse embryo, thus helping bolster researchers' knowledge of the extent of gene transcription. The results of their study, published in the journal PLoS Biology, will give scientists the information they need to determine co-expressions of genes as well as to recognise links between genes that play a crucial role in both development and disease. The study was funded in part by the EUREXPRESS ('European consortium to generate a web-based gene expression atlas by RNA [ribonucleic acid] in situ hybridization') project, which clinched almost EUR 11 million under the 'Life sciences, genomics and biotechnology for health' Thematic area of the EU's Sixth Framework Programme (FP6). EUREXPRESS created the expression data for more than 20,000 genes by RNA in situ hybridisation on sagittal sections from mouse embryos. In this study, researchers led by the Telethon Institute of Genetics and Medicine (TIGEM) in Italy included expression data for more than 18,000 coding genes for hundreds of anatomical structures in an interactive, comprehensive and open digital gene expression atlas. They successfully identified tissue-specific and tissue-overlapping gene networks. The information obtained provides new insight into developing structures, including the telencephalon (cerebrum), which is a large region within the brain attributed to various functions like motor. The team successfully correlated disease phenotypes to sites of expression of underlying genes, and extracted information to shed light on the complex segmental organisation in the mammalian brain. Thanks to the EUREXPRESS-generated atlas, the cellular resolution allowed the team to identify the gene markers that characterise the molecular subdivision of organs and novel putative markers of the haematopoietic lineage; and facilitate the comprehensive organism-wide mapping of a key developmental signalling pathway. 'The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organisation for the hypothalamus, and insight on the Wnt [signalling pathway] involved in renal epithelial differentiation during kidney development,' the authors write. TIGEM Professor Andrea Ballabio says, 'This work was only possible due to the close collaboration of all scientists involved and nicely illustrates the success a coordinated and collaborative effort can achieve. The gene expression atlas will be an important guide to discover gene function and disease mechanisms.' Commenting on the collaborative effort of the study, Professor Stylianos E Antonarakis of the University of Geneva in Switzerland and co-author says: 'The size of the task required a team of specialists whose combination of different expertise was needed to achieve an output that is greater than the sum of the parts. The freely available data and the impressive images will be of great help to all researchers working on the function of the genome and the molecular causes of the myriads of genetic disorders.' The researchers point out that genomic research has fuelled our understanding of physiological and pathophysiological processes, ranging from infectious diseases to cancer. Production of large datasets and the integration of information found within are fundamental aspects of this approach, they explain. 'Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function,' they write. 'Progress in understanding gene networks is driven by massive parallel approaches that capture the complexity of a gene network as a whole.' In future, these data could be used for identifying regional differences that are hard to pin down within structurally complex organs, and expression signatures for specific cell populations. Experts from France, Germany, Italy, Spain, Switzerland, the UK and the US contributed to this study.For more information, please visit: EUREXPRESS:http://www.eurexpress.orgTelethon Institute of Genetics and Medicine (TIGEM):http://www.tigem.it/PLoS Biology:http://www.plosbiology.org/home.actionTo download the PLoS Biology article, click:http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000582 (here)
Countries
Switzerland, Germany, Spain, France, Italy, United Kingdom, United States
