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IPSEP, the epigenomics platform dedicated to plants
There are several epigenomics platforms around the world, for example at the University of Michigan (The Epigenomics Core, 2015) or at the Medical College of Cornell University (Epigenomics Core Facility, 2015). However, these platforms, on the one hand, are specialized in the treatment of mammalian samples and, on the other hand, do not propose a three-dimensional analysis of the chromatin structure for the moment. In this context, the Institute of Plant Sciences Paris-Saclay (IPS2) relied on the expertise of its researchers to create the first epigenomics platform specialized in the treatment of plant samples and offering the possibility to analyze the 3D chromatin organization, based on the projects started since 2015. This platform, called IPSEP and officially created in January 2016, is designed to propose a set of epigenomic and bioinformatic analysis solutions for a very large range of plant species. Through technological and scientific monitoring, IPSEP also aims to develop innovative biochemical and genomic methodologies in relation to the needs of plant biology research.
Epigenetic regulation in plants, adaptation to their environment and agriculture
Epigenetic regulations refer to regulations of heritable characters independently of the DNA sequence. In recent years, the term has been more widely used to also define the processes of regulation of gene expression and genomic functions that are superimposed on DNA sequence information. Epigenetic information is contained and mediated by the distribution of cytosine modifications such as DNA methylation (5mC) and hydroxymethylation (5hmC), post-translational modifications of different histones and other proteins, as well as by the 3D topology of chromatin in the nucleus of the eukaryotic cell.
Our understanding of the mechanisms involved and of the role of epigenetic heritability in plants is increasing rapidly. Many studies have emphasized the importance of these regulations not only in the adaptation of plants to their environment and in response to biotic or abiotic stresses, but also in the control of agronomic traits of interest. Moreover, the maintenance and stabilization of these traits in elite lines or F1 hybrids are also major agricultural issues and currently research efforts aim at improving our knowledge of the epigenetic mechanisms involved. The manipulation of epigenetic pathways in plants is considered today as a tool for the creation of phenotypic variability on characters of multigenic origin, without altering the DNA sequence, and as a means of removing the reproductive incompatibility between certain varieties or species to better exploit biodiversity. Epigenetic research thus offers great potential for the development of innovative and effective approaches for the improvement of crops species.
Constant technological development...
As a result of the development of technologies for rapid and integrated profiling of both genotype and epigenotype, it is now possible to produce and improve the resources needed to dissect the mechanisms involved in phenotype regulation and to clarify the contribution of epigenetics in these questions. However, the implementation and mastery of the various techniques dedicated to these analyzes are particularly demanding and require not only excellent expertise in biochemistry and genomics but also specific and expensive equipment.
The study of epigenetic regulation in a variety of developmental and environmental contexts has taken a large part in the research conducted at IPS2. The teams of Moussa Benhamed ("Cell Cycle, Chromatin and Development") and Martin Crespi ("Non-coding RNAs") have developed in recent years a wide range of methodological approaches to study these regulations. ChIPseq, a method routinely used to analyze histone modifications, has been optimized for the study of transcription factors (Jégu et al., 2017; Veluchamy et al., 2016; Neyret-Khan et al., 2013; Benhamed et al., 2012). In addition , IPS2 has also worked on the optimization of HiC, to detect the 3D structure of DNA-DNA interactions in chromatin (Veluchamy et al., 2016) and ChIRP (Chromatin RNA- based purification), for the analysis of RNA-chromatin interactions (Ariel et al., 2014, Ariel et al., in preparation). More recently, a collaboration with the group of Abdelhafid Bendahmane ("Flower and carpel development") has associated epigenomic methods with laser microdissection of melon tissues (Latrasse et al., 2017) to add a "cell-type specific" dimension to IPSEP. The human resources and equipment necessary for the development of these approaches have been funded by these different teams, under the overall coordination of M. Benhamed, scientific manager of the platform.
... for an integrated study of epigenetic processes
Thanks to these technical and technological developments, the services currently offered by the IPSEP platform allow a genome-wide analysis:
DNA Methylation (MeDIP-seq)
Histone modifications (ChIP-seq)
Transcription factor binding sites (TF-ChIP-seq)
Nucleosome positioning (Mnase-seq)
Open chromatin regions (ATAC-seq)
3D chromatin structure (Hi-C and ChIA-PET)
nc RNA binding sites (ChIRP-seq)
If you wish to integrate the study of epigenetic regulations into your research projects, do not hesitate to contact the IPSEP platform to benefit from its expertise!
Ariel F., Jegu T., Latrasse D., Romero-Barrios N., Christ A., Benhamed M., Crespi M. (2014). Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop. Molecular Cell 55(3): 383-396.
Benhamed M., Herbig U., Ye T., Dejean A., Bischof O. (2012). Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nature Cell Biology 14(3): 266-+.
Jegu T., Veluchamy A., Ramirez-Prado J.S., Rizzi-Paillet C., Perez M., Lhomme A., Latrasse D., Coleno E., Vicaire S., Legras S., Jost B., Rougee M., Barneche F., Bergounioux C., Crespi M., Mahfouz M.M., Hirt H., Raynaud C., Benhamed M. (2017). The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biology 18.
Latrasse D., Rodriguez-Granados N.Y., Veluchamy A., Mariappan K.G., Bevilacqua C., Crapart N., Camps C., Sommard V., Raynaud C., Dogimont C., Boualem A., Benhamed M., Bendahmane A. (2017). The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo. Epigenetics & Chromatin 10.
Neyret-Kahn H., Benhamed M., Ye T., Le Gras S., Cossec J.C., Lapaquette P., Bischof O., Ouspenskaia M., Dasso M., Seeler J., Davidson I., Dejean A. (2013). Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation. Genome Research 23(10): 1563-1579.
Veluchamy A., Jegu T., Ariel F., Latrasse D., Mariappan K.G., Kim S.K., Crespi M., Hirt H., Bergounioux C., Raynaud C., Benhamed M. (2016). LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. Plos One 11(7).