Livrables
Summer schools will take place during year 2 and 4 devoted to develop specific issues in depth. The Chromatin3D PIs and invited scientists worldwide will discuss research on relevant topics. These will be mandatory for all Chromatin3D ESRs. Summer schools will be ~4 days long at a resort to isolate the group and facilitate interactions and will precede the relevant annual Chromatin3D meetings. In this way, the ESRs will be in a superb position to take full advantage and digest the excellent possibilities that an international meeting offers. Each summer school will have the participation of at least half of the Chromatin3D PIs plus 3-7 invited speakers. At least one of such invitees will focus on ethical issues and at least one on academia-industry interactions and biotech/pharma work. The first summer school will be coordinated by FORTH in collaboration with the Weizmann Institute in the island of Crete. The University of Edinburgh in collaboration with IDIBELL will coordinate the second summer school. Both summer schools will be open to 20 additional participants. Chromatin3D’s ESRs will be actively involved in organising both schools participating in the advertisement of the events and selecting external speakers.
Business and entrepreneurship courseBusiness and entrepreneurship training addresses issues on intellectual property, entrepreneurship and business development. This mandatory course will be aimed at getting the ESRs to think about how novel ideas can be commercialized. It will involve a staged series of exercises, which move from vision and idea to definition of work to be done through protecting intellectual property, raising finance, marketing and sales. The whole series will engage the ESRs by getting them to work in teams and develop a business-plan guided by the training team. Case studies will be delivered by entrepreneurs and venture capitalists. The business-training course will be held in Milan (IIT) and will cover topics such as patent law applied to smart materials, drug discovery and diagnostics, public health and entrepreneurship. The CEOs of all non-academic participants (Diagenode, UD-GenoMed, Mosaiques, ACS, Exiqon, LifeGlimmer, YR, SB Science Management) will contribute on commercialization.
Visits and secondments of ESRsSpecialized, task-centred learning during secondments: All Network partners have defined 15 individual projects facilitating task-centered learning, which has been shown to be most effective. Each project and its scientific training activities are outlined below. For each ESR the secondment organization was chosen on the basis of scientific relevance, cohesion of distinct experimental approaches and complementarities in addressing the ESR’s individual project aims. Note the interdisciplinarity of most projects and the tight interactions between several groups that ensure the high level training of each ESR. The high prevalence of ESRs to the network is indicative of the high training priorities of this Network and the willingness of all PIs from both the academic and non-academic sector to directly mentoring the proposed tasks. Details of secondments are listed in Table 4.1d for each individual research project.
Recruitment of ESRsESRs will be hired within the first five months of the network contract in order to allow three years to complete a doctoral degree and to be able to participate in the training activities outlined in section B.2.2. Recruiting clever, well-educated and dedicated candidates for research in life sciences is an increasing problem for most European research institutions. We will therefore invest all possible efforts into recruiting the best candidates, from Europe as well as other parts of the world. All scientists-in-charge will form a Recruitment Committee and will have a first meeting in connection with the Initial Network Meeting (project month 1). The recruitment committee will be responsible for WP1 (“Recruitment”). This includes organizing the recruitment of 15 ESRs within the first five months. Furthermore, the committee will ensure that the recruitment procedure is in line with the principles set out in the European Charter for Researchers (http://ec.europa.eu/euraxess/index.cfm/rights/europeanCharter) and in the Code of Conduct for the Recruitment of Researchers (http://ec.europa.eu/euraxess/index.cfm/rights/codeOfConduct). Vacancies will be advertised through the Euraxess - Researchers in Motion website (ec.europa.eu/euraxess), Euro Science Jobs (www.eurosciencejobs.com), the PI’s and ETN homepages, in scientific journals, at major Academic institutions, conferences, through e-mails, e-mailing lists from relevant conferences etc. The Recruitment Committee in collaboration with the respective responsible scientist at the host organisation will draft the advertisement. Candidates will be asked to specify first, second and third priority host institutes. Advertising text will lay out the scientific and training nature of the Chromatin3D ETN, will be explicit about eligibility issues and will specifically -though not narrowly- outline the expected qualifications of applicants. All partners will be involved in the recruitment process and will select fellows on the criteria of their motivation, interests, degree, grades and experience. Applications (i.e. letter of intent, CVs and recommendation letters) will be collected by the Recruitment Committee and distributed to all participants. Short-listed candidates will be invited to visit the lab of the PI they are most interested in joining. Interviews during the visit will be carried out by teleconferencing to include at least one other participant of the Network as an interviewer. Problems with recruitment: If a partner cannot find an eligible candidate, acceptable applicants to other partners (not elected) may be offered the chance. If this is unsuccessful, the position will be re-announced with less specific requirements regarding disciplinary background. If no candidate for a position is found before month 12 of the project, that position will be cancelled, and crucial tasks will be done by staff at the host institution and other network trainees within the relevant WP.
Attendance of ESRs in international conferences & symposiaInternational exposure of Chromatin3D ESRs will be expected since they will attend at least two top international events of their choice to present their work. This will allow students to gain experience, interact with the scientific community and present their work to an audience. Conferences and symposia can include the CSHL conference series, Biotech workshops and meetings, Keystone and EMBO workshops, etc. Attendance to biotech/pharma and other health-science industry meetings will be strongly encouraged.
Final Network ConferenceOrganization of a final Network Conference: A widely publicized international meeting will be organized in Greece to coincide with the closing Network Meeting to sum up and promote the research goals attained by the Network and to place those in a broader scientific perspective by inviting other scientists from all areas related to the themes of the network to participate in the conference. The meeting will be open to 100-150 external attendees. Funding will be covered by registration fees of external attendees and by sponsorship. For this event 25 senior scientists will be invited to present their work and share with the Chromatin3D participants their knowledge and experience. Moreover the ESRs will actively participate in the organisation of the meeting, inviting external speakers and thus getting an ideal opportunity to have a direct contact for their future Postdoctoral training. Additional members of other networks (many of the Chromatin3D PIs already participate in other FP7-ITN networks) will be invited to participate to this meeting. During this concluding meeting, ESRs will present their completed research. A final open forum session will allow ESRs and the PIs to discuss the training programme. ESRs will be encouraged to suggest improvements of the programme. PIs will discuss the possibility of future collaborations.
International Course on Laboratory Animal ScienceThe International Course on Laboratory Animal Science at BSRC A.FLEMING in Athens will be obligatory to those ESRs where an animal welfare course is not available locally. The programme duration is one week and is organized on an annual basis by the A.FLEMING (http://www.animalfacility.eu). The course includes a theoretical understanding on the needs, the limitations and the ethical issues in animal experimentation. A theoretical and practical course in statistics and management of an experiment involving animals will be programmed. A practical session involving animal handling will be included. The workshop will end with a written test and a certificate will be delivered to successful ESRs including appropriate ECTS grades.
Project Management courseThe project management course will cover planning, project management, creativity in research, group dynamics, networking, developing self-awareness and stress management. We will invite a representative from the International Project Management Association (IPMA-Nijkerk/Netherlands, http://ipma.ch) specialized in the management of publicly funded projects and the exploitation of results. This course will also include contributions from UD-GenoMed, Diagenode, Mosaiques, ACS, Exiqon, Yellow Research and SB Science Management and will be mandatory for all ESRs.
Workshop 3: “Developmental Programming and Reprogramming”Location: Munich Organizer: Peter Becker Benefit to the ESRs and other trainees: This workshop aims to familiarize ESRs and other trainees on the different epigenetic studies that focus on developmental processes and especially the regulation of diverse differentiation pathways involved in embryonic stem cells and the choice of different cell fates. One representative from Diagenode (Helene Pendeville) will discuss the different analysis platforms the company offers for the study of such modifiers. One representative from ACS (J.Oliver) will discuss cell-based assays with the use of primary cells that retain the memory of their tissue of origin and reflect its state of health or disease. Provisional Program George Garinis (Heraklion) NER Factors in Development and Disease Wolf Reik (Cambridge) Epigenetic reprogramming in mammalian development Peter Becker (Munich) Epigenome stratification during Drosophila embryogenesis *Helene Pendeville (Liege) DNA methylation and demethylation studies John Strouboulis (Athens) GATA factors in erythroid cell differentiation Edith Heard (Paris) X chromosome inactivation in mouse embryonic stem cells Wouter de Laat (Utrecht) The pluripotent genome in three dimensions Rolf Ohlsson (Stockholm) Cancer stem cell epigenome analysis *Jo Oliver (Ayr) Primary cell-based assays
Workshop 1: “Folding chromatin in Three Dimensions”Location: Stockholm Organizer: Rolf Ohlsson Benefit to the ESRs and other trainees: This workshop will expose young researchers from all over Europe to a series of talks covering the current view we share for the three dimensional organization of the eukaryotic genome. New technologies employed worldwide and within the network (Chromosome conformation capture/3C-based) will be discussed. One speaker from SME will also cover different technology platforms (*H.Pendeville). Provisional Program Daniela Rhodes (Cambridge) Chromatin structure and recognition Wendy Bickmore (Edinburgh) Folding chromatin during development and disease Edith Heard (Paris) X-chromatin structure and dynamics during X inactivation Peter Fraser (Cambridge) Single molecule chromosome structure analysis Babis Spilianakis (Heraklion) Regulation of CD4 cell differentiation in three dimensions Peter Becker (Munich) Assembly of (hetero-)chromatin during early embryogenesis *Helene Pendeville (Liege) Automation of epigenetic assays Eran Segal (Rehovot) Nucleosome Disfavouring Sequences Alter Gene Expression
Bioethics CourseThe Bioethics course that will be held in Munich/LMU will draw on lectures organized by the Munich Ethics Referral Center. Lectures will cover topics, including ethics of stem cells and cloning research, genetic testing and selection of human beings and ethical regulations in biomedicine.
Workshop 4: “Epigenetic modifiers and genome integrity”Location: Edinburgh Organizer: Wendy Bickmore Benefit to the ESRs and other trainees: This workshop aims to expose ESRs and other trainees on the different epigenetic modifications involved in regulating physiological processes and sustain the homeostasis of the eukaryotic genome. Two speakers from SMEs will participate and discuss novel advances in the field (Bálint L. Bálint from UD-GenoMed and Hazel Pinheiro from Exiqon). Provisional Program Peter Verrijzer (Rotterdam) Chromatin and transcription control by Nucleotide Biosynthetic Enzymes Bruno Amati (Milan) Chromatin-regulatory enzymes and cancer genomes Manel Esteller (Barcelona) miRNA profiling and epigenetic control of tumorigenesis Babis Spilianakis (Heraklion) Epigenetic modulators of CD4 T cell plasticity *Bálint L. Bálint (Debrecen) Gene expression and data integration George Garinis (Heraklion) DNA damage in aging and cancer: new tricks with old bricks *Hazel Pinheiro (Vedbaek) microRNA Inhibitor products for functional analysis of microRNAs
Open Lab DayOpen Lab Days will be organized at which the ESRs invite the general public to the laboratories and present their research projects and results “hands on” to a general audience. Whenever possible, the open lab days will be synchronized and advertised together with the institutions’ “Open Doors” days organized by the different partner universities in order to maximize publicity and impact. Each ESR will be required to organize lab demonstrations and a short public lecture on her/his project.
I. Scientific writing and presentation courseScientific writing and presentation skills: on a continuous basis, there will be several opportunities for perfecting scientific writing and presentation skills through participation in local group meetings and Journal Clubs, as well as in network-wide meetings and other international conferences. Training in manuscript and proposal writing is also part of the local individual research-driven training activity as the ESRs will be expected to write-up their own results for publication and future fellowship applications with direct guidance by their supervisors. The partner organizations, LifeGlimmer, Yellow Research and SB Science management will be major contributors in this task.
Communication courseCommunication training will be based on lectures organized by the network on support and guidance of ESRs. Communication training includes training of writing skills, presentation and oral communication skills. Writing skills is usually addressed individually as part of each research project. The trainers will give practical advice on public speaking techniques and on how to deliver presentations to different target audiences or stakeholders. The ESRs will be able to apply their newly gained communication skills in scientific activities such as the summer schools.
Workshop 2: “Cancer Epigenomics”Location: Milan Organizer: Bruno Amati Benefit to the ESRs and other trainees: The aim of this workshop is to introduce students from all over Europe the different experimental models that are used in order to study chromatin-based modifiers in the cause of cancer. Two speakers from SMEs (Hazel Pinheiro from Exiqon, Bálint L. Bálint from UD-GenoMed) will cover topics related to biomarker discovery approaches and valorization of results for commercial applications. Provisional Program Manel Esteller (Barcelona) PharmacoEpigenetics: Genes and Drugs Rolf Ohlsson (Stockholm) Chromosomal Networks: New Perspectives of Cancer Epigenomics Bruno Amati (Milan) Myc-induced lymphomagenesis Tony Kouzarides(Cambridge) Targeting epigenetic pathways in the treatment of cancer *Hazel Pinheiro (Vedbaek) miRNA profiling services for biomarker discovery *Bálint L. Bálint (Debrecen) Epigenetic & epigenomic analysis services for cancer diagnostics Kristian Helin (Copenhagen) Role of hydroxymethylation in stem cells and cancer Valerio Orlando (Rome) Epigenetic control of noncoding genome in disease
Chromatin3D website. The website will provide comprehensive information about the science, technology and members of the network, its nodes and ongoing activities. It will include a popular science section featuring popular-science articles, blogs, interactive animations, and videos/podcasts of public lectures, many of which will be sourced from other outreach activities detailed below. Each ESR will be expected to take part in the development and maintenance of the website.
Chromatin3D NewsletterAnnual Chromatin3D newsletter aimed at high-school and undergraduate university students as well as the wider public. All members of Chromatin3D (ESRs, PIs) will contribute to this format. The newsletter will popularize Chromatin3D’s activities by explaining its societal, technological and scientific impacts. It will include features about important scientific results and technical developments, interviews with ESRs and PIs about their work and career perspectives, as well as articles about Chromatin3D’s activities in general. The newsletter will appear in print and in electronic form to be distributed via the website and interested subscribers (schools, universities, individuals and companies).
Facebook Chromatin3D pageChromatin3D Facebook Group. Chromatin3D’s ESRs will set up an open Facebook group through which they can communicate among themselves and the general public. This social network complements the more technical internet-based transfer-of-knowledge and communication facilities on the Chromatin3D newsgroup as well as the network website. The Facebook group will feature personal sections for each ESR detailing their research projects, work environments as well as personal motivations, experiences and thoughts to serve as examples for the careers of upcoming young scientists. The group will be accessible to the public who will thus be enabled to engage online with Chromatin3D’s ESRs, e.g., by posting science-related questions, reading about the scientific progress, learning about other outreach activities, etc.
Podcasts & VideocastsSelected public lectures, lab demonstrations and interviews with ESRs and PIs will be recorded on video and/or audio to set up a comprehensive record of Chromatin3D’s scientific activities accessible to the public via the Internet. These recordings will be made available to the general public via the network website, the Facebook group and direct postings to forums such as YouTube.
Publications
Auteurs:
I. Tzelepis, M. Martino, A. Göndör
Publié dans:
Chromatin Regulation and Dynamics, 2017, Page(s) 1-34, ISBN 9780-128033951
Éditeur:
Elsevier
DOI:
10.1016/b978-0-12-803395-1.00001-0
Auteurs:
Ilias Tzelepis, Mirco Martino and Anita Göndör
Publié dans:
Chromatin Regulation and Dynamics; Translational Epigenetic Series, 2016, ISBN 978-0-12-803395-1
Éditeur:
Elsevier
Auteurs:
Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B Becker
Publié dans:
Life Science Alliance, Numéro 1/1, 2017, Page(s) e201800024, ISSN 2575-1077
Éditeur:
LifeScience Alliance
DOI:
10.26508/lsa.201800024
Auteurs:
David J. Hanly, Manel Esteller, María Berdasco
Publié dans:
Philosophical Transactions of the Royal Society B: Biological Sciences, Numéro 373/1748, 2018, Page(s) 20170074, ISSN 0962-8436
Éditeur:
Royal Society of London
DOI:
10.1098/rstb.2017.0074
Auteurs:
Iwona Belczacka, Agnieszka Latosinska, Justyna Siwy, Jochen Metzger, Axel S. Merseburger, Harald Mischak, Antonia Vlahou, Maria Frantzi, Vera Jankowski
Publié dans:
Scientific Reports, Numéro 8/1, 2018, Page(s) 8:5227, ISSN 2045-2322
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41598-018-23585-y
Auteurs:
Iwona Belczacka, Martin Pejchinovski, Magdalena Krochmal, Pedro Magalhães, Maria Frantzi, William Mullen, Antonia Vlahou, Harald Mischak, Vera Jankowski
Publié dans:
PROTEOMICS - Clinical Applications, Numéro 18 October 2018, 2018, Page(s) 1800111, ISSN 1862-8346
Éditeur:
Wiley - VCH Verlag GmbH & CO. KGaA
DOI:
10.1002/prca.201800111
Auteurs:
Iwona Belczacka, Agnieszka Latosinska, Jochen Metzger, David Marx, Antonia Vlahou, Harald Mischak, Maria Frantzi
Publié dans:
Mass Spectrometry Reviews, Numéro 38/1, 2017, Page(s) 49-78, ISSN 0277-7037
Éditeur:
John Wiley & Sons Inc.
DOI:
10.1002/mas.21572
Auteurs:
Stavros Bashiardes, Anastasia Godneva, Eran Elinav, Eran Segal
Publié dans:
Current Opinion in Biotechnology, Numéro 51, 2018, Page(s) 57-63, ISSN 0958-1669
Éditeur:
Elsevier BV
DOI:
10.1016/j.copbio.2017.11.013
Auteurs:
Pierbruno Ricci, Pedro Magalhães, Magdalena Krochmal, Martin Pejchinovski, Erica Daina, Maria Rosa Caruso, Laura Goea, Iwona Belczacka, Giuseppe Remuzzi, Muriel Umbhauer, Jens Drube, Lars Pape, Harald Mischak, Stéphane Decramer, Franz Schaefer, Joost P. Schanstra, Silvia Cereghini, Petra Zürbig
Publié dans:
Scientific Reports, Numéro 9/1, 2019, Page(s) 9:2225, ISSN 2045-2322
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41598-019-38713-5
Auteurs:
David Marx, Jochen Metzger, Jérôme Olagne, Iwona Belczacka, Stanislas Faguer, Magali Colombat, Holger Husi, William Mullen, Wilfried Gwinner, Sophie Caillard
Publié dans:
PROTEOMICS - Clinical Applications, Numéro 1800091C, 2019, Page(s) 1800091, ISSN 1862-8346
Éditeur:
Wiley - VCH Verlag GmbH & CO. KGaA
DOI:
10.1002/prca.201800091
Auteurs:
Daphna Rothschild, Omer Weissbrod, Elad Barkan, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul I. Costea, Anastasia Godneva, Iris N. Kalka, Noam Bar, Smadar Shilo, Dar Lador, Arnau Vich Vila, Niv Zmora, Meirav Pevsner-Fischer, David Israeli, Noa Kosower, Gal Malka, Bat Chen Wolf, Tali Avnit-Sagi, Maya Lotan-Pompan, Adina Weinberger, Zamir Halpern, Shai Carmi, Jingyuan Fu, Cisca Wijmenga, Alex
Publié dans:
Nature, Numéro 555/7695, 2018, Page(s) 210-215, ISSN 0028-0836
Éditeur:
Nature Publishing Group
DOI:
10.1038/nature25973
Auteurs:
Maria Frantzi, Agnieszka Latosinska, Iwona Belczacka, Harald Mischak
Publié dans:
Expert Review of Proteomics, Numéro 16/1, 2018, Page(s) 49-63, ISSN 1478-9450
Éditeur:
Future Drugs Ltd.
DOI:
10.1080/14789450.2018.1547193
Auteurs:
David Marx, Jochen Metzger, Martin Pejchinovski, Ryan Bruce Gil, Maria Frantzi, Agnieszka Latosinska, Iwona Belczacka, Silke Sophie Heinzmann, Holger Husi, Jerome Zoidakis, Matthias Klingele, Stefan Herget-Rosenthal
Publié dans:
Seminars in Nephrology, Numéro 38/1, 2018, Page(s) 63-87, ISSN 0270-9295
Éditeur:
W. B. Saunders Co., Ltd.
DOI:
10.1016/j.semnephrol.2017.09.007
Auteurs:
Zeevi, D., Korem T., Godneva, A., Bar, N. ,Segal, E
Publié dans:
Nature, Numéro 27 March 2019, 2019, ISSN 1476-4687
Éditeur:
NatureResearch
DOI:
10.1038/s41586-019-1065-y
Auteurs:
Attila Horvath, Bence Daniel, Lajos Szeles, Ixchelt Cuaranta-Monroy, Zsolt Czimmerer, Lilla Ozgyin, Laszlo Steiner, Mate Kiss, Zoltan Simandi, Szilard Poliska, Nikolas Giannakis, Emanuele Raineri, Ivo G Gut, Benedek Nagy, Laszlo Nagy
Publié dans:
Nucleic Acids Research, Numéro 2019 1, 2019, Page(s) 2019 1, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkz118
Auteurs:
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
Publié dans:
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Numéro 1861/1, 2018, Page(s) 14-28, ISSN 1874-9399
Éditeur:
Elsevier BV
DOI:
10.1016/j.bbagrm.2017.11.003
Auteurs:
Stratigi K, Chatzidoukaki O, Garinis GA.
Publié dans:
Mechanisms of Ageing and Development, 2016, ISSN 0047-6374
Éditeur:
Elsevier BV
DOI:
10.1016/j.mad.2016.09.008
Auteurs:
1) Belczacka I, Latosinska A, Frantzi M, and Harald Mischak H.
Publié dans:
UROTODAY, Numéro May 10 2018, 2018, Page(s) May 10 2018
Éditeur:
DIGITAL SCIENCE PRESS, INC.
Auteurs:
Zelenka T.
Publié dans:
VESMIR, Numéro Vesmír 97, 34, 2018/1, 2018, Page(s) Vesmír 97, 34, 2018/1
Éditeur:
https://vesmir.cz/cz/casopis/archiv-casopisu/2018/cislo-1/prostorova-organizace-chromatinu.html
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