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THE CNRGH LABORATORIES

Epigenetic and Environment

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Published on 23 May 2017

​​Team leader: Jörg Tost
E-mail: jorg.tostat​cng​.fr

The Epigenetic and Environment Laboratory (LEE) aims at obtaining a complete picture of the epigenetic changes in various contexts pertinent to human health.

The Laboratory team has set up a robust process, unique in France, for the identification and validation in human diseases of the epigenetic modifications of which DNA methylation, miRNA and chromatin conformation changes. The LEE masters a variety of bisulfite genome sequencing technologies for analysis of DNA methylation and hydroxymethylation and works in close cooperation with the CNRGH high- and intermediate-throughput platforms. The technologies may be adapted to the various quantities of material at the outset down to less than 50 ng of isolated DNA. The associated bioinformatics pipelines also available at the LEE for processing the data and identifying the methylated regions undergo continuous refinement. Another technology currently used in numerous projects is the Illumina BeadChip 450K for which a dedicated bioinformatics pipeline has been developed. The DNA methylation changes thus identified are subsequently validated using the pyrosequencing technology developed by the Laboratory. RNAs are analyzed by small RNA‑seq or using a panel of qPCR tests based on LNA. The modifications of the miRNA and methylation of DNA are compared with the changes in the histones and other DNA binding proteins by ChIP-seq. while the regulatory components are identified using the innovative ATAC-seq. test based on transposase. While the team initially focused on the epigenetic changes in cancer, the team's objective has evolved over the last 3 years with a focus on analysis of epigenetic changes in complex human diseases including autoimmune diseases, inflammatory diseases and allergic diseases together with neurodegenerative diseases. A second focus is on the epigenome changes caused by environmental factors such as viruses (e.g. HIV), bacteria or low-dose radiation exposure.​

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Quantitative analysis of DNA
methylation by pyrosequencing
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Quantification by real-time PCR of
DNA libraries for whole genome
​sequencing of methylation

The technologies available for whole-genome analysis are as follows:  whole genome bisulfite sequencing, MeDIP-seq, smallRNA-seq, ChIP-seq, ATAC-seq, Illumina BeadChip 450K

The technologies available for analysis of specific loci:  pyrosequencing (methylation, mutations), E-ice-COLD-PCR (mutations), qPCR (miRNA)​