Final Report Summary - EPITRAITS (Epigenetic regulation of economically important plant traits)
Final Publishable Summary Report Marie Curie ITN EpiTRAITS (Epigenetic regulation of economically important plant traits)
Mission of EpiTRAITS
The mission of the EpiTRAITS project, coordinated by the University of Amsterdam (UvA), is to improve the career prospects and employability of young researchers by providing a custom-made training program: a dedicated combination of research and transferrable skills required to pursue a career in academic and industrial environments. At the scientific level we trained young researchers in epigenetic gene regulation and flowering in the model plant Arabidopsis thaliana and the crop plants maize (Zea mays) and barley (Hordeum vulgare). Epigenetic gene regulation confers stability of gene expression patterns through cell divisions while allowing changes in expression in response to environmental or developmental cues. Although changes in epigenetic gene regulation are a major cause for trait variation, there are no rational strategies to utilize this knowledge for crop breeding purposes. EpiTRAITS focused on one key plant trait that impacts crop yield, flowering, which is epigenetically controlled. The scientific program bridges the gap between fundamental and applied research by translating results from epigenetic research in model organisms to improved technologies for crop breeding and molecular diagnostic tools.
EpiTRAITS consortium
The EpiTRAITS consortium, which ran successfully from October 2012 to September 2016, consisted of 13 Partners (including 4 companies), 5 Associated Partners (3 industrial), 11 employed early stage researchers and 3 experienced researchers in 8 different countries (www.epitraits.eu). The partners consisted of research groups at the Universities of Amsterdam (UvA), Wageningen (WU), Duesseldorf (UDUS), Polish Academy (IPG-PAS), Nottingham (UNOTT), and Berlin (FUB), and the institutes Max Planck Institute for Plant Breeding Research (MPIPZ), Instituto Nacional de Investigaciones Agrarias (INIA), Institut National de la Recherche Agronomique (INRA) and the companies Biomol-Informatics, Diagenode, KeyGene and PhytoWelt. The fellows were appointed after a joint recruitment procedure consisting of a special web portal and interviews in Amsterdam featuring different activities. The joint procedure significantly strengthened enduring collaboration between the partners, and resulted in the E(S)Rs forming a genuine team before they were officially appointed. To ensure an optimal project start, most fellows began March 2013, when also the first network-wide training event and kick-off meeting were organized. The first training events provided the fellows with project management skills, the scientific background on the research and technologies to be performed and used within the EpiTRAITS project, and the knowledge and skills required to be successful in a company.
To optimize the training program and promote collaboration between partners and fellows, Annual Meetings were organized to monitor the fellow’s progress through presentations and evaluation discussions. During the first year an extra meeting, linked with the European Workshop on Plant Chromatin, ensured the fellows got on track. Monthly video conferences were attended by the PIs and representatives of the fellows, to discuss and monitor the issues raised during the project. Together with the MC-ITN CHIP-ET (www.chip-et.eu) EpiTRAITS co-organised, the international Epigenetic & Chromatin Regulation of Plant Traits Conference, January 2016, in Strasbourg (www.epi2016) at which the results of EpiTRAITS were presented to the scientific community and interested companies. In 2016, most fellows attended a final meeting.
EpiTRAITS training
To improve the fellows’ career prospects, both in academia and companies, the fellows also attended four other blocks of courses and workshops, which were usually organized around the annual meetings. The topics ranged from ethics, presentation, dissemination, writing and statistics skills to entrepreneurship, next-generation sequencing, bioinformatics, image analysis and modeling. Also, the fellows were seconded to other partners to promote scientific excellence and exploit the infrastructure and interdisciplinary expertise within the consortium, thereby advancing their projects and acquiring new knowledge and skills. Progress was reported half-yearly, followed by an oral discussion between the fellow, daily supervisor, mentor from the ITN and one of the members of the external advisory board (EAB). This resulted in the Personal Career Development Plan (PCDP; template developed by the EpiTRAITS) being updated with individual project descriptions, secondments, and training events, workshops & conferences attended. At the end the fellows received a certificate indicating they successfully accomplished the EpiTRAITS training.
EpiTRAITS research
The scientific data generated by EpiTRAITS provides insight into gene regulation at multiple levels, including the DNA, chromatin and nuclear organization level. A multidisciplinary approach was used, ranging from molecular to cell biology, genetics, biochemistry, bioinformatics, statistics, advanced microscopy, image analysis and mathematical modeling. Scientific highlights include:
• The UvA and MPIPZ used newly generated and available epigenomic profiles to predict new regulatory sequences in Zea mays. The function of a subset of these sequences is now being examined.
• The UvA successfully developed a combined immunolabeling-FISH protocol for plant tissues.
• Proteomics analysis pursued by WU, INIA and UDUS/FUB, using baits of interest, successfully found interacting proteins, including transcription factors and chromatin-associated proteins.
• IPG-PAS developed a pipeline for the analysis of chromatin conformation capture (4C) data. The scripts are published with a basic documentation at https://github.com/DimitrisZisis/4CseqR.
• UNOTT successfully embedded gene expression models within static multicellular models of shoot apical meristems undergoing the floral transition. These show that the relevant genes are expressed in the correct zones, and that only two positional cues are necessary to achieve that result.
• INRA developed generic spatial statistical tools to be used for analysing the spatial organization of biological objects in different systems. Results obtained with the pipeline reveal a complex, multi-scale organization of chromocenters within the nuclear space and how this is affected by mutations.
• Diagenode successfully developed and commercialized an Arabidopsis and Universal Plant ChIP-seq kit. Both kits greatly facilitate ChIP experiments on plant material.
• KeyGene successfully developed a cost effective, complexity reduction technique called methylation Sequence-Based Genotyping (mSBG) to epigenotype segregating plant populations.
• Phytowelt identified candidate genes that may be linked to plant regeneration potential.
Dissemination
The EpiTRAITS consortium has disseminated their results and knowledge with the general public via several outreach activities (see www.epitraits.eu). One highlight is four movies written and directed by the fellows; two are voiced-over in several languages and are available on different websites, including www.epitraits.eu. Currently published papers will be supplemented by others in the near future. People involved in EpiTRAITS will continue their outreach activities.
Impact EpiTRAITS
The EpiTRAITS consortium provided the fellows with: a broad range of skills and knowledge; an extensive professional network within Europe; the ability to maximally profit from the multidisciplinary expertise within EpiTRAITS; enhanced expertise and scientific output; and improved career prospects. EpiTRAITS also established and strengthened collaborations between the academic and private partners, and other MC-ITNs, which will aid the establishment of future projects and collaborations. Epi2016 positively contributed to strengthening collaborations at the European level. EpiTRAITS also resulted in commercial success: Diagenode developed and commericalized plant-specific ChIP-seq kits, and KeyGene developed the mSBG technique that is now used in their laboratories.
The Mid-term Review of EpiTRAITS took place in Amsterdam in July 2014 and received a very good review. The External Advisory Board, consisting of four members, judged EpiTRAITS as an excellent exemplar for ITNs, and considered the project extremely well managed, the commitment shown by the supervisors and fellows exemplary, the collaboration and interaction within the consortium, and scientific output impressive. Most importantly, the scientific progress as well as the personal development made by the fellows was judged very impressive overall.
For more details see www.epitraits.eu
Mission of EpiTRAITS
The mission of the EpiTRAITS project, coordinated by the University of Amsterdam (UvA), is to improve the career prospects and employability of young researchers by providing a custom-made training program: a dedicated combination of research and transferrable skills required to pursue a career in academic and industrial environments. At the scientific level we trained young researchers in epigenetic gene regulation and flowering in the model plant Arabidopsis thaliana and the crop plants maize (Zea mays) and barley (Hordeum vulgare). Epigenetic gene regulation confers stability of gene expression patterns through cell divisions while allowing changes in expression in response to environmental or developmental cues. Although changes in epigenetic gene regulation are a major cause for trait variation, there are no rational strategies to utilize this knowledge for crop breeding purposes. EpiTRAITS focused on one key plant trait that impacts crop yield, flowering, which is epigenetically controlled. The scientific program bridges the gap between fundamental and applied research by translating results from epigenetic research in model organisms to improved technologies for crop breeding and molecular diagnostic tools.
EpiTRAITS consortium
The EpiTRAITS consortium, which ran successfully from October 2012 to September 2016, consisted of 13 Partners (including 4 companies), 5 Associated Partners (3 industrial), 11 employed early stage researchers and 3 experienced researchers in 8 different countries (www.epitraits.eu). The partners consisted of research groups at the Universities of Amsterdam (UvA), Wageningen (WU), Duesseldorf (UDUS), Polish Academy (IPG-PAS), Nottingham (UNOTT), and Berlin (FUB), and the institutes Max Planck Institute for Plant Breeding Research (MPIPZ), Instituto Nacional de Investigaciones Agrarias (INIA), Institut National de la Recherche Agronomique (INRA) and the companies Biomol-Informatics, Diagenode, KeyGene and PhytoWelt. The fellows were appointed after a joint recruitment procedure consisting of a special web portal and interviews in Amsterdam featuring different activities. The joint procedure significantly strengthened enduring collaboration between the partners, and resulted in the E(S)Rs forming a genuine team before they were officially appointed. To ensure an optimal project start, most fellows began March 2013, when also the first network-wide training event and kick-off meeting were organized. The first training events provided the fellows with project management skills, the scientific background on the research and technologies to be performed and used within the EpiTRAITS project, and the knowledge and skills required to be successful in a company.
To optimize the training program and promote collaboration between partners and fellows, Annual Meetings were organized to monitor the fellow’s progress through presentations and evaluation discussions. During the first year an extra meeting, linked with the European Workshop on Plant Chromatin, ensured the fellows got on track. Monthly video conferences were attended by the PIs and representatives of the fellows, to discuss and monitor the issues raised during the project. Together with the MC-ITN CHIP-ET (www.chip-et.eu) EpiTRAITS co-organised, the international Epigenetic & Chromatin Regulation of Plant Traits Conference, January 2016, in Strasbourg (www.epi2016) at which the results of EpiTRAITS were presented to the scientific community and interested companies. In 2016, most fellows attended a final meeting.
EpiTRAITS training
To improve the fellows’ career prospects, both in academia and companies, the fellows also attended four other blocks of courses and workshops, which were usually organized around the annual meetings. The topics ranged from ethics, presentation, dissemination, writing and statistics skills to entrepreneurship, next-generation sequencing, bioinformatics, image analysis and modeling. Also, the fellows were seconded to other partners to promote scientific excellence and exploit the infrastructure and interdisciplinary expertise within the consortium, thereby advancing their projects and acquiring new knowledge and skills. Progress was reported half-yearly, followed by an oral discussion between the fellow, daily supervisor, mentor from the ITN and one of the members of the external advisory board (EAB). This resulted in the Personal Career Development Plan (PCDP; template developed by the EpiTRAITS) being updated with individual project descriptions, secondments, and training events, workshops & conferences attended. At the end the fellows received a certificate indicating they successfully accomplished the EpiTRAITS training.
EpiTRAITS research
The scientific data generated by EpiTRAITS provides insight into gene regulation at multiple levels, including the DNA, chromatin and nuclear organization level. A multidisciplinary approach was used, ranging from molecular to cell biology, genetics, biochemistry, bioinformatics, statistics, advanced microscopy, image analysis and mathematical modeling. Scientific highlights include:
• The UvA and MPIPZ used newly generated and available epigenomic profiles to predict new regulatory sequences in Zea mays. The function of a subset of these sequences is now being examined.
• The UvA successfully developed a combined immunolabeling-FISH protocol for plant tissues.
• Proteomics analysis pursued by WU, INIA and UDUS/FUB, using baits of interest, successfully found interacting proteins, including transcription factors and chromatin-associated proteins.
• IPG-PAS developed a pipeline for the analysis of chromatin conformation capture (4C) data. The scripts are published with a basic documentation at https://github.com/DimitrisZisis/4CseqR.
• UNOTT successfully embedded gene expression models within static multicellular models of shoot apical meristems undergoing the floral transition. These show that the relevant genes are expressed in the correct zones, and that only two positional cues are necessary to achieve that result.
• INRA developed generic spatial statistical tools to be used for analysing the spatial organization of biological objects in different systems. Results obtained with the pipeline reveal a complex, multi-scale organization of chromocenters within the nuclear space and how this is affected by mutations.
• Diagenode successfully developed and commercialized an Arabidopsis and Universal Plant ChIP-seq kit. Both kits greatly facilitate ChIP experiments on plant material.
• KeyGene successfully developed a cost effective, complexity reduction technique called methylation Sequence-Based Genotyping (mSBG) to epigenotype segregating plant populations.
• Phytowelt identified candidate genes that may be linked to plant regeneration potential.
Dissemination
The EpiTRAITS consortium has disseminated their results and knowledge with the general public via several outreach activities (see www.epitraits.eu). One highlight is four movies written and directed by the fellows; two are voiced-over in several languages and are available on different websites, including www.epitraits.eu. Currently published papers will be supplemented by others in the near future. People involved in EpiTRAITS will continue their outreach activities.
Impact EpiTRAITS
The EpiTRAITS consortium provided the fellows with: a broad range of skills and knowledge; an extensive professional network within Europe; the ability to maximally profit from the multidisciplinary expertise within EpiTRAITS; enhanced expertise and scientific output; and improved career prospects. EpiTRAITS also established and strengthened collaborations between the academic and private partners, and other MC-ITNs, which will aid the establishment of future projects and collaborations. Epi2016 positively contributed to strengthening collaborations at the European level. EpiTRAITS also resulted in commercial success: Diagenode developed and commericalized plant-specific ChIP-seq kits, and KeyGene developed the mSBG technique that is now used in their laboratories.
The Mid-term Review of EpiTRAITS took place in Amsterdam in July 2014 and received a very good review. The External Advisory Board, consisting of four members, judged EpiTRAITS as an excellent exemplar for ITNs, and considered the project extremely well managed, the commitment shown by the supervisors and fellows exemplary, the collaboration and interaction within the consortium, and scientific output impressive. Most importantly, the scientific progress as well as the personal development made by the fellows was judged very impressive overall.
For more details see www.epitraits.eu