Evolution of transcriptional regulation
Our team creates and maintains the genomic resources of the Ensembl project and is responsible for data management for a number of large-scale international projects, including the 1000 Genomes Project and, in collaboration with the Brazma team, the International Mouse Phenotyping Consortium. We also collaborate on the development of EMBL-EBI’s major variation databases, including the European Genome-phenome Archive (EGA) and the DGVa database of copy number and structural variation. All of these resources are publicly available and are widely used by the scientic community and by the team itself as part of our research into evolution, epigenetics and transcriptional regulation.
Our specific research projects focus on the evolution of transcriptional regulation. Recently we have expanded ‘comparative regulatory genomics’ techniques including mapping the same DNA–protein interactions in matched tissues in multiple species to understand how gene regulation has evolved while the tissue-level functions are largely conserved. We are also interested in the role of chromatin conformation in tissue-specic gene regulation and have investigated both the CTCF and cohesin complex in this context.
Future projects and goals
With the issue of major datasets from the EU-funded Blueprint project and the NIH-funded KOMP2 project, we continue to play an end-to-end role in major genomics projects from raw-data management for the project to summary- data presentation to the wider scientic community.
Our research projects are expanding in number of species, tissues and specific DNA–protein interactions. We will also focus on understanding the differentiation process and components of cell- and tissue-specific regulation. We will address these questions both in the context of our established collaborative projects with the Odom group at the University of Cambridge and as part of other collaborations, including larger EU-funded projects.
1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65.
Schmidt, D., et al. (2012) Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335-348.
Schmidt D, et al. (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 20, 578-588.