An ambitious EC-funded research initiative on epigenetics advancing towards systems biology

Our research focuses on high-throughput epigenetics and systems biology of T lymphocyte ontogeny, building on the multifaceted epigenotypes of cis-regulatory units while turned on or off during cell-development. We (i) use primary T cells and deep sequencing of enriched DNAs and RNAs to profile histone modifications, nucleosome positioning, transcription factor (TF) binding and genomic expression within such units; (ii) develop predictive simulations for the dynamics of these several variables; (iii) by genetic manipulations and knockdown interference, test these principles and their functional relevance. Using 3C-derived technologies, we also explore how these variables may impact on long-range regulatory interactions; and higher-order chromosomal architecture.  
Additional programs include the definition, via endogenous tagging, of TF-anchored nucleo-protein complexes and their location in mouse ES cells and derived tissues; the study of DNA recombination in normal and leukemic T cells, also combining epigenetics and mathematical modelling; and the implementation of dedicated computational tools.

List of the PhDs and Postdocs involved in research on EpiGeneSys projects:

Dr. Jinsong JIA: Post-doc; Epigenetic dynamics a developmentally regulated genes during T-cell differentiation.
Dr. Joaquin Zacarias Cabeza: Post-doc; Transcription-dependent generation of a specialized chromatin structure initiated by the TCRb gene enhancer.
Aleksandra Pekowska: PhD Student; Epigenetic signatures of active enhancers during T lymphocyte ontogeny.
Frederic Koch: PhD Student; Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.
Larysa Kazheunikava: PhD Student; Characterization of genome-wide TLX3 target genes in T-cell acute leukemias.
Romain Fenouil; Nicolas Descostes: PhD Students