Integrative omics to study gene expression regulation

Head of the project

Delphine Plieger

Gene expression is regulated in part by the incorporation of histone variants and by the dynamic modification of histones by various chemical groups. This double layer of regulation can be studied using proteomics. To confidently carry out such analyses, we established a database containing an exhaustive and non-redundant list of histone sequences for mouse and human (El Kennani et al., Epigenetics and Chromatin 2017). We further developed a method for the targeted proteomic analysis of a large number of variants of histones H2A and H2B, including sequences that differ by a single amino acid (El Kennani et al., Epigenetics and Chromatin 2018). Another project focusing on subtle amino acid variations has been carried out with Christophe Battail (IMAC, BCI) in the context of cancer: it aimed at measuring the relative amounts of WT versus mutated proteins in the case of heterozygous mutations, and relied on integrating RNA-seq and proteomic analyses.

Our research activities also aim at studying the effects of recently described histone post-translational modifications (PTMs) on gene expression. We started such explorations in the context of mouse spermatogenesis (collaboration Julie Cocquet, Institut Cochin, Paris), a differentiation process in which Lys crotonylation was originally reported (Tan M. et al., Cell 2011). Quite unexpectedly, the proteomic analysis of histones extracted from three cellular stages of mouse spermatogenesis revealed that crotonylation was of similar stoichiometry to acetylation on histone H3 Lysine 27 (H3K27). Since H3K27ac marks active transcription when present at promoters, and also marks active distal enhancers, we combined our proteomics data with ChIP-seq data obtained on H3K27cr to get its localization on the genome, and to public RNA-seq data to study the effect of this histone PTM on gene expression (collaboration with Christophe Battail). Additional public ChIP-seq datasets were collected to compare the association of various chromatin-binding proteins with H3K27cr and with H3K27ac. Metabolomics data on the donor groups for acylations, namely acyl-coA, were also acquired (collaboration with LEMM, CEA Saclay), to try to correlate the abundance of these analytes with histone PTM stoichiometries. Finally, our study indicates both synergistic and specific actions of each histone modification at promoters and distal enhancers (Crespo M et al., under review). In the future, we wish to build on our acquired expertise in integrating diverse omics data to study the effect of original histone PTMs on gene expression regulation in biomedical contexts.

Publications

  • El Kennani S, Adrait S, Shaytan A, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D*, Govin J*. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics & Chromatin, 2017
  • El Kennani S, Adrait A, Permiakova O, Hesse AM, Ialy-Radio C, Ferro M, Brun V, Cocquet J, Govin J*, Pflieger D*. Systematic quantitative analysis of H2A and H2B variants by targeted proteomics. Epigenetics & Chromatin, 2018
  • El Kennani S*, Crespo M, Govin J, Pflieger D*. Proteomic analysis of histone variants and their PTMs: strategies and pitfalls. Proteomes, 2018
  • Marion Crespo, Annelaure Damont, Melina Blanco, Emmanuelle Lastrucci, Sara El Kennani, Côme Ialy-Radio, Laila El Khattabi, Samuel Terrier, Mathilde Louwagie, Sylvie Kieffer-Jaquinod, Anne-Marie Hesse, Christophe Bruley, Sophie Chantalat, Jérôme Govin, François Fenaille, Christophe Battail*, Julie Cocquet*, Delphine Pflieger*. Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes. Under review.

Funding

  • CEA PhD fellowship to Sara El Kennani
  • UGA PhD fellowship to Marion Crespo
  • ANR.