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Chromatin in Plants – European Training and Mobility

Final Report Summary - CHIP-ET (Chromatin in Plants – European Training and Mobility)

Chromatin in Plants, European Training and Mobility (CHIP-ET)
Project ID: FP7-PEOPLE-2013-ITN607880 (2013-2017)
Mission Statement
The research in the CHIP-ET network is focused on the study of protein complexes that modulate chromatin structure to activate RNA polymerase II–mediated transcript elongation. Research addresses how these complexes cross-talk to developmental and environmental stimuli such as light signals and the circadian clock and transcriptionally regulate specific pathways and responses. The interactome of the complexes is determined, as well as their genome-wide target genes and the common and specific components in their molecular networks. The impact of perturbation of complex components or regulators on plant development and stress tolerance is analyzed in the Arabidopsis model. Improved agronomic traits such as improved field performance and yield in crop epilines, selected for improved immunity or energy use efficiency, will be correlated with their epigenomes and putative epialleles determined.
The CHIP-ET consortium consisted of five academic and one industrial partners; six early stage researchers (ESRs) and one experienced researcher (ER) were employed in four different countries and originated from five different countries, taking into account gender equality and matching educational training with research projects and motivation. The partners were represented by principal investigators at the universities, research centers, and company, i.e. Mieke Van Lijsebettens (scientific coordinator, Center of Plant Systems Biology, VIB/UGent, Belgium), Klaus Grasser (training manager, Department of Cell Biology and Plant Biochemistry, University of Regensburg,UR, Germany), Andreas Houben (Department Breeding Research,, IPK Gatersleben, Germany), Wen-Hui Shen (Plant Molecular Biology Institute of CNRS, IBMP-CNRS, Strasbourg, France), Paloma Mas (Center for Research in Agricultural Genomics, CRAG, Barcelona, Spain) and Marc De Block (BioScience Research Bayer CropScience, Gent, Belgium); all partners were work package coordinators. Existing bilateral collaboration formed the basis from which the network was consolidated and new collaborations were initiated.
A central goal of the CHIP-ET consortium was preparing the trainees (ER, ESRs) for a future career in academia and private enterprise. At regular meetings during the entire project period starting with the kick-off meeting in Gatersleben (April, 2014) to the final network meeting associated with the European Plant Chromatin Workshop in Vienna (Mai, 2017) the trainees were offered a wide variety of opportunities to broaden their scientific horizon and learn to know state-of-the-art experimental approaches. These comprised advanced microscopy, laser microdissection, luminescence assays, protein-protein and protein-nucleic acids interaction assays, fitness assays, epigenome technologies and large dataset analyses. During the network meetings, based on status presentations the trainee’s research progress was openly discussed among the team of PIs and trainees. There also the best way of organising secondments in the partner laboratories was reasoned to maximise the benefit for the research projects as well as to optimise the exploitation of the expertise and infrastructure within the network. To become accustomed to think beyond the own project, the trainees were motivated to supervise student practicals and BSc/MSc projects. All trainees participated in international scientific conferences/symposia/workshops, also presenting their results. Moreover, by attending offered courses/seminars the trainees expanded their portfolio of soft skills including communication, good scientific practice, self-organisation, time/conflict management, intellectual property-related issues and writing of job/funding applications. The trainees were involved in the organisation of the network meetings and of the international conference “Epigenetic & Chromatin Regulation of Plant Traits” in Strasbourg, 2016, co-organised with the ITN EpiTRAITS. Commercial exploitation of results, patenting or entrepreneurship were illustrated in a network visit to the industrial partner. All activities were incorporated in the personal career development plan that was monitored by the training manager, and regularly discussed at the network meetings.
The UR successfully affinity purified the interactome of transcript elongation factors and identified by mass spectrometry other transcript elongation factors, chromatin modifiers, and strikingly, components of the transcript processing machinery such as splicing and export.
VIB/UGent, UR, and IBMP-CNRS discovered that transcript elongation factors and histone modifiers have specific functions in plant development, such as in photomorphogenesis, circadian clock, flowering time and in response to stress conditions.
IBMP-CNRS investigated crosstalk of histone modifications and demonstrated combinatorial function of different histone methylations in transcription activation of flowering time genes.
VIB/UGent, UR and IPK optimized technology for plant models and crops which related to cytosine methylome profiling and bioinformatics pipeline, protein purification, and fluorescence in situ hybridization, respectively.
IPK analyzed the function of a chromatin condensation component to decipher the interplay between interphase structure and global gene transcription and chromatin modifications.
CRAG studied the epigenetic regulation of the plant circadian clock using a model plant. The effect of mutations in essential players of chromatin mark deposition in the rhythmic oscillation of core clock genes was monitored using marker genes in bioluminescence assays. This knowledge was shared in collaborative projects with other partners.
Bayer CropScience selected epilines in canola and rice based on tolerance to high doses of the plant hormone, salicylic acid or on improved energy use efficiency. Bayer CropScience and VIB/UGent detected activated epigenomes and putative epialleles that correlated with transcriptional networks and with the improved agronomic traits in those epilines.
Dissemination activities included acknowledging the CHIP-ET funding in publications resulting from the CHIP-ET research projects in international peer-reviewed journals, at oral and poster presentations at international symposia and at network workshops that were public. An important dissemination activity was the international conference “Epigenetic & Chromatin Regulation of Plant Traits” in Strasbourg ( local organizer A. Berr of the CHIP-ET network and scientific organizers M. Van Lijsebettens of the CHIP-ET network and M. Stam of the EpiTRAITS ITN network. The meeting created a forum for the 120 European and international participants to share and discuss recent research results and technological experiences which was further stimulated by the presence of company boots. The CHIP-ET network ( was presented to the public at large during open days outreach activities organized at several partner institutes (CRAG, IPK, CNRS).
The partners provided multi-disciplinary cutting-edge technologies and know-how in chromatin research in high quality research projects to the fellows in order to further science in Europe, develop their careers and prepare them for scientific or entrepreneurial leadership. The international meeting organized by the CHIP-ET and EpiTRAITS ITN networks was a forum for networking within and outside Europe. No doubts new consortia and collaborations are in the making that will create synergy and added value for Europe. World-wide annual crop losses by biotic and abiotic stresses are substantial and the research in the CHIP-ET network showed that important agronomic traits such as fitness and yield have an epigenetic basis, epigenetic and genetic markers for crop breeding are to be expected in the near future. In addition, the developed methylome profiling method will facilitate and speed up identification of combinatorial epialleles early in the breeding programs.
Mieke Van Lijsebettens, Scientific Coordinator (Belgium)