Minutes of the EPIC meeting in Philadelphia

Minutes EPIC organizational meeting Philadelphia May 2014

The meeting started out with a review of the minutes of the last meeting and of recent EPIC activities by Doris Wagner (University of Pennsylvania). The meeting then focused on the discussion of the future of the EPIC initiative and what activities EPIC should actively be involved in going forward. The NSF-funded EPIC RCN ends in April 2015. Briefly, it was decided that (1) EPIC will continue to coordinate development of EPIC CoGe browsers for deposition, analysis and comparison of plant epigenomic datasets. In addition, (2) EPIC will hold yearly symposia alternating between the Americas, Asia and Europe, to further develop and enhance plant epigenetic and epigenomic research. Moreover, (3) EPIC and its membership will actively seek interaction and exchange with breeders and industry representatives to identify needs for crop enhancement that can be addressed by harnessing epigenetic approaches. Finally (4) EPIC will become a membership organization, which will hold town hall-style organizational meetings to discuss community needs. These meetings will take place in conjunction with the yearly symposia.

Eric Lyons (iPlant, University of Arizona) reported on the current features of the EPIC CoGe browser that was developed jointly by Eric Lyons and Matt Bomhoff and Brian Gregory (University of Pennsylvania) with his former graduate student Fan Li. Initial funding for this initiative was provided by the Gordon and Betty Moore Foundation, with cyberinfrastructure support by iPlant. All present agreed that the EPIC CoGe browser is developing very well and this initiative is a key focus of EPIC. Going forward, pipelines will be developed for automated analysis of raw sequencing data prior to upload to the EPIC CoGe browsers. Also additional query and data visualization tools will be developed. [Eric and Brian – I had to leave frequently during this part, can you please add any additional future directions that I missed here?]. One current bottleneck is data ingestion, both more automated ways of data upload and more user participation in this process will be pursued. In addition, institution of a user fee for data kept private post publication may encourage data upload in the public domain. Eric asked all users to provide feedback on any additional functionalities they wish to see developed for EPIC CoGe.

More and more epigenomic datasets are being generated in model and non-model plant species (Jose Gutierrez-Marcos reported on an impressive array of activities underway in this regard in Europe), hence there is a need to develop CoGe browsers for diverse plant species. Eric and Brian are working on EPIC CoGe browsers for Arabidopsis, maize and soybean. For maize they are collaborating with Nathan Springer/Matt Vaughn, who are funded for maize browser development. These CoGe browsers are envisioned as future modules of AIP (Arabidopsis Information Portal). Xiao-Feng Cao (CAS, Beijing, China) reported on progress towards a rice CoGe browser to be developed in China using the platforms developed by Eric and Brian. The UK had expressed an interest in developing a wheat CoGe browser and Korea one for a Solanaceae species. There was no additional information available on these latter two initiatives.

One concern is future funding of EPIC CoGe browser development and maintenance. Eric Lyons and Brian Gregory submitted a PGRP grant, whose emphasis is noncoding RNAs, with one aim dedicated to further browser development. Several large dataset generating EPIC members wrote letters of support for this grant. Eric has some funding for browser development through a USDA-funded project and has applied for a data-driven discovery grant to the GBMF to support EPIC CoGe browser development. A future funding source for this endeavor, once CoGe has been widely adopted, is a possible ‘fee for service’ approach. Rob Martienssen and Doris Wagner will be proactive in helping to ensure continued funding for EPIC and EPIC CoGe.

At the last EPIC meeting, it had been decided that we will publish a series of Epigenetics methods papers, which should be linked also to the EPIC website. Roger Deal discussed his efforts to come up with a model to make this work at Frontiers, where he is editor of a methods journal. He will continue to work on the best way to do this.

Scott Michaels (University of Indiana) discussed his efforts to organize regular EPIC symposia in the US. Several venues were interested in a Plant Epigenetics/Noncoding RNA type conference. It was decided that Keystone Symposia will be pursued further, with a first EPIC Keystone Symposium to be held in 2016. Scott will organize this symposium together with Doris Wagner and one other EPIC member (Nathan Springer, if he agrees). The symposium proposal will be submitted by early June 2014. The group briefly discussed topics Scott had proposed. EPIC planning Committee members have been enthusiastic about this proposal and are suggesting possible symposium speakers. It was discussed whether this meeting could possibly be held closer to the summer (May?) to allow temporal spacing with meetings in Europe and Asia. In Europe there already exists a symposium, which is held every two years, the ‘European workshop on Plant Chromatin’. This symposium will next be held in late August of 2015 in Sweden (Lars henning and Caludia Köhler are the organizers). Vincent Colot (ENS, Paris, France) will inquire about the possibility of linking this conference to EPIC. For Asia, several possibilities were discussed, including the CSHL plant genome meetings in China. Xiao-Feng Cao would be able to organize a local organizational meeting linked to such an EPIC symposium [did I get this right Xiao-feng?]. The symposia speakers and attendees are anticipated to include industry representatives, breeders, and ecologists [is that right, Scott?].

Brian Hauge from Monsanto discussed industry interests in plant epigenetics/epigenomics. On key step will be additional informational meetings where industry members can learn more about the recent advances in plant epigenetics/epigenomics and plant epigenetics researchers can learn more about key industry needs/questions. The latter include control of transgene stability in germplasms, apomixes/hybrid vigor, genotype and environment interacts that determine traits. It would be best if many companies could partake in such a meeting, including Dupont, Syngenta, Mendel, Bayer, BASF etc. A “Plant Epigenomics and Agriculture” Banbury Conference has tentatively been planned from October 2014, this effort is spearheaded by Rob Martienssen. Eric Richards (BTI, Cornell) emphasized that genotype to phenotype is also a key priority of NSF, as are links from plant epigenetics/epigenomics data to biological function.

Finally, in regards to the governance of EPIC, it was decided that the EPIC organizational meetings to be held in conjunction with the yearly symposia should be open to all attendees to foster communication and community representation. The community would elect the EPIC president elect who, together with the current president (three organizers are needed for keystone symposia) would organize the next symposium and organizational meeting, oversee EPIC CoGe browser development and keep the EPIC website current. It may be advisable to elect members from different continents to facilitate organization of international symposia. It would be advantageous if support staff were available to help coordinate these activities, the group envisioned that support staff could be hired in the future be through industry and funding agency sponsorship or by forming a society which collects yearly membership dues. Such funding may also help defract some of the travel cost of conference attendees. Time and money permitting, one additional EPIC organizational meeting will be held in 2015 in conjunction with a symposium already being planned.

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