From haplotype to phenotype: a systems integration of allelic variation, chromatin state and 3D genome data

Project Information

HAP-PHEN

Grant agreement ID: 637587

DOI

10.3030/637587

Project closed

EC signature date 7 August 2015

Start date 1 September 2015

End date 31 August 2020

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 500 000,00

EU contribution

€ 1 500 000,00

Coordinated by

STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Other (1)

WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation

Author(s): Ning Qing Liu, Michela Maresca, Teun van den Brand, Luca Braccioli, Marijne M.G.A. Schijns, Hans Teunissen, Benoit G. Bruneau, Elphège P. Nora, Elzo de Wit
Published in: 2019
Publisher: bioRxiv
DOI: 10.1101/731141

Peer reviewed articles (14)

The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse

Author(s): Lucas J.T. Kaaij, Fabio Mohn, Robin H. van der Weide, Elzo de Wit, Marc Bühler
Published in: Cell, Issue 178/6, 2019, Page(s) 1437-1451.e14, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.08.007

LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS

Author(s): Li Li, Pieter C van Breugel, Fabricio Loayza-Puch, Alejandro Pineiro Ugalde, Gozde Korkmaz, Naama Messika-Gold, Ruiqi Han, Rui Lopes, Eric P Barbera, Hans Teunissen, Elzo de Wit, Ricardo J Soares, Boye S Nielsen, Kim Holmstrøm, Dannys J Martínez-Herrera, Maite Huarte, Annita Louloupi, Jarno Drost, Ran Elkon, Reuven Agami
Published in: Nucleic Acids Research, Issue 46/8, 2018, Page(s) 4213-4227, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky087

Enhancer hubs and loop collisions identified from single-allele topologies

Author(s): Amin Allahyar, Carlo Vermeulen, Britta A. M. Bouwman, Peter H. L. Krijger, Marjon J. A. M. Verstegen, Geert Geeven, Melissa van Kranenburg, Mark Pieterse, Roy Straver, Judith H. I. Haarhuis, Kees Jalink, Hans Teunissen, Ivo J. Renkens, Wigard P. Kloosterman, Benjamin D. Rowland, Elzo de Wit, Jeroen de Ridder, Wouter de Laat
Published in: Nature Genetics, Issue 50/8, 2018, Page(s) 1151-1160, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0161-5

TADs as the Caller Calls Them

Author(s): Elzo de Wit
Published in: Journal of Molecular Biology, Issue 432/3, 2020, Page(s) 638-642, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2019.09.026

The structural basis for cohesin–CTCF-anchored loops

Author(s): Yan Li, Judith H. I. Haarhuis, Ángela Sedeño Cacciatore, Roel Oldenkamp, Marjon S. van Ruiten, Laureen Willems, Hans Teunissen, Kyle W. Muir, Elzo de Wit, Benjamin D. Rowland, Daniel Panne
Published in: Nature, Issue 578/7795, 2020, Page(s) 472-476, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1910-z

High-throughput identification of human SNPs affecting regulatory element activity

Author(s): Joris van Arensbergen, Ludo Pagie, Vincent D. FitzPatrick, Marcel de Haas, Marijke P. Baltissen, Federico Comoglio, Robin H. van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen J. Bussemaker, Bas van Steensel
Published in: Nature Genetics, Issue 51/7, 2019, Page(s) 1160-1169, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-019-0455-2

Developing landscapes: genome architecture during early embryogenesis

Author(s): Robin H van der Weide, Elzo de Wit
Published in: Current Opinion in Genetics & Development, Issue 55, 2019, Page(s) 39-45, ISSN 0959-437X
Publisher: Elsevier BV
DOI: 10.1016/j.gde.2019.04.009

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

Author(s): Geert Geeven, Hans Teunissen, Wouter de Laat, Elzo de Wit
Published in: Nucleic Acids Research, 2018, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky443

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

Author(s): Lucas J.T. Kaaij, Robin H. van der Weide, René F. Ketting, Elzo de Wit
Published in: Cell Reports, Issue 24/1, 2018, Page(s) 1-10.e4, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.06.003

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension

Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Published in: Cell, Issue 169/4, 2017, Page(s) 693-707.e14, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.04.013

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

Author(s): Peter Hugo Lodewijk Krijger, Bruno Di Stefano, Elzo de Wit, Francesco Limone, Chris van Oevelen, Wouter de Laat, Thomas Graf
Published in: Cell Stem Cell, Issue 18/5, 2016, Page(s) 597-610, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2016.01.007

A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation

Author(s): Gozde Korkmaz, Zohar Manber, Rui Lopes, Stefan Prekovic, Karianne Schuurman, Yongsoo Kim, Hans Teunissen, Koen Flach, Elzo de Wit, Giorgio G Galli, Wilbert Zwart, Ran Elkon, Reuven Agami
Published in: Nucleic Acids Research, Issue 47/18, 2019, Page(s) 9557-9572, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz675

Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation

Author(s): Ahmed M.O. Elbatsh, Eugene Kim, Jorine M. Eeftens, Jonne A. Raaijmakers, Robin H. van der Weide, Alberto García-Nieto, Sol Bravo, Mahipal Ganji, Jelmi uit de Bos, Hans Teunissen, René H. Medema, Elzo de Wit, Christian H. Haering, Cees Dekker, Benjamin D. Rowland
Published in: Molecular Cell, Issue 76/5, 2019, Page(s) 724-737.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2019.09.020

CTCF: a Swiss-army knife for genome organization and transcription regulation

Author(s): Luca Braccioli, Elzo de Wit
Published in: Essays in Biochemistry, Issue 63/1, 2019, Page(s) 157-165, ISSN 0071-1365
Publisher: Portland Press, Ltd.
DOI: 10.1042/ebc20180069