The mission of the Functional Genomics Laboratory (LGF) is to characterize the mechanisms underlying complex human diseases. The etiology of multifactorial complex diseases involves, in particular, genetic factors. Whole-genome association studies have enabled identification of numerous genetic variations associated with several of those diseases. However, the variations only partially explain the observed inheritability. The missing inheritability component may be explained by disturbances of the epigenome for which the physiological medium is chromatin, which has been reported to impair the expression of genes related to the disease.
Chromatin, which results from the association between DNA and histone proteins, conditions the access of the regulatory regions of DNA to transcription factors. Numerous studies have shown that remodeling of chromatin at the level of those regions has a marked impact on the transcription program. Comparative analysis of the degree of chromatin opening, healthy subjects vs. patients, is thus an approach which may generate major information on the transcription status of genes and the mechanisms underlying their deregulation. The enzymes that modify chromatin may be targeted by pharmaceutical inhibitors. This constitutes a promising approach in therapeutic research.
We are currently focusing on the study of inflammatory diseases. We are conducting comparative analyses of the chromatin derived from patients and controls. We identify open chromatin sites on the genome scale by DNase-seq, which is currently the most sensitive method. We are implementing strategies to identify changes in accessibility in the regulatory regions and to define a chromatin signature associated with a given disease.
A change in the openness state of chromatin in patients may impair the recruitment of transcription factors at the regulation site and induce changes in gene expression. This has led us to analyze the transcriptome of patients by RNA-seq. We then incorporate the results of the transcriptome analyses with the data on chromatin opening status with the aim of investigating for mechanisms underlying the deregulation of gene expression.
We are also investigating for connections between epigenome impairment and genotypes: by incorporating genotyping data in our analysis, we are investigating whether genetic polymorphisms are liable to influence chromatin openness status.
Our Laboratory has acquired advanced expertise in whole-genome approaches. We master the following technologies:
- DNase-seq, ATAC-seq and FAIRE-seq.
- ChIP-seq
- Bisulfite conversion and genotyping chips 450K
- RNA-seq (total or messenger, oriented or non-oriented)
We also master the techniques of molecular biology (cloning, vector manipulation), cell biology (immunofluorescence), biochemistry (chromatin purification, fractionation methods) and cell culturing (primary cultures and cell lines).