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ChromDesign-ITN: Chromatin topology studies in mouse ES and human leukemia cell lines (subproject ESR13); Hosting institution: Diagnose, Liege, Belgium

Project Description

"ChromDesign” is a European innovative and interdisciplinary Research and Training network, which aims to characterize the impact of the 3D chromatin organization on gene regulation during cellular differentiation and in several human disorders, and to train junior researchers in the biomedical field, either in academia or in the private sector. The "ChromDesign" training programme will foster mobility across countries, disciplines and sectors. Through secondments and network-events, we will ensure that all ESRs have opportunities for exposure to different disciplines and environments: academia, industry, design and communication, hospitals, publishing, and non-for-profit funding entities. Most network training will be based around five summer and winter schools that combine hands-on research workshops, academic lectures as well as transferable skills, and innovation and entrepreneurship training sessions.

Description subproject ESR13:

Understand how changes in chromatin topology occur during cell differentiation with HT technologies. The organization of the nuclear chromatin is extremely relevant to the biological function at the gene level and at the global nuclear level.
ESR13 will investigate how the spatial organization of chromatin affects gene regulation and differentiation. Firstly developing an optimized Hi-C kit to study chromatin interacting domains in mouse embryonic pluripotent and differentiated stem cells to identify which interacting domains are involved in cell differentiation.
As proof of concept, ESR13 will use the results obtained using ESCs. They will be fully differentiated into cardiomyocytes and compared with the functional and genome-wide analysis data published by the coordinator, L. Di Croce (P1a). Secondly, ESR13 will study the role of the chromatin in genome regulation in normal conditions and in disease by using Hi-C technology to study chromatin topological associated domains (TADs) in leukaemia and differentiated induced leukaemia cell lines.

Chipmentation for Chromatin Immunoprecipitation sequencing in low cell number. Hi-C analysis. FISH. RNA-seq. ATAC-seq.

Expected Results:
Identification of chromatin interacting domains affecting cell differentiation. Development of a Hi-C kit.

Planned Secondments:

CRG, Spain (1 month): Hi-C data analyses and functional comparison and functional analyses.
Characterisation of interacting domains in differentiated induced leukaemia cells.

UCPH, Denmark (3 weeks):
Integration of ChIP-seq data and ATAC-seq data in leukemic cell model system.

Eligibility criteria:

• Applicants may be a national of a Member State, of an Associated Country or of any other third country.

• The candidate should hold an academic degree that enables her/him to undertake doctoral studies. Preference is given to applicants with MSc or equivalent degree.

• At the time of recruitment* by the host organisation, candidates must be in the first four years (full-time equivalent research experience**) of their research careers and not yet have been awarded a doctoral degree.

• At the time of recruitment* by the host organisation, candidates must not have resided or carried out their main activity (work, studies, etc.) in the country of their host organisation for more than 12 months in the 3 years immediately prior to the reference date.


Funding Notes

• Depending on the hosting institute, individual projects start between November 2018 and August 2019.

• The positions are fully funded for 36 months by the European Comission under the H2020 Marie Curie Innovative Training Network Programme.

• Marie Curie ITNs provide a highly competitive salary to the ESR, including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance.


Laczik M, Hendrickx J., Veillard A.C., Tammoh M., Marzi S. and Poncelet D. Iterative fragmentation improves the detection of ChIP-seq peaks for inactive histone marks. Bioinformatics and Biology Insights 10:209-224, 2016.

Berguet G, Hendrickx J, Sabatel C, Laczik M, Squazzo S, Mazon Pelaez I, Saxena R, Pendeville H, Poncelet D. Automating ChIP-seq experiments to generate epigenetic profiles on 10,000 HeLa cells. J Vis Exp. 2014; (94): 52150.

Veillard A.C., Datlinger P., Laczik M., Squazzo S. and Bock C. Diagenode® premium RRBS technology: cost-effective DNA methylation mapping with superior coverage. Nature Methods 13:184, 2016.

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