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Of Dots and Stripes: The Morse Code of Micro-C Reveals the Ultrastructure of Transcriptional and Architectural Mammalian 3D Genome Organization

 Li-Hsin Chang , Daan Noordermeer
Molecular Cell, 2020, 78 (3), pp.376--378. ⟨10.1016/j.molcel.2020.04.021⟩
Article dans une revue hal-02995878v1

GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth

 Leanne Li , Qiqun Zeng , Arjun Bhutkar , José A. Galván , Eva Karamitopoulou , et al.
Cancer Cell, 2018, 33 (4), pp.736--751.e5. ⟨10.1016/j.ccell.2018.02.011⟩
Article dans une revue hal-02180785v1
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Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq)

 Mélody Matelot , Daan Noordermeer
Polycomb Group Proteins: Methods and Protocols, 1480, Springer Science+Business Media New York, pp.223-241, 2016, 9781493963782. ⟨10.1007/978-1-4939-6380-5_20⟩
Chapitre d'ouvrage hal-01412298v1
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ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocations

 Coline Arnould , Vincent Rocher , Aldo S Bader , Emma Lesage , Nadine Puget , et al.
2022
Pré-publication, Document de travail hal-03818730v1
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Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

 Li-Hsin Chang , Sourav Ghosh , Andrea Papale , Jennifer M Luppino , Mélanie Miranda , et al.
Nature Communications, 2023, 14, pp.5615. ⟨10.1038/s41467-023-41265-y⟩
Article dans une revue hal-04239007v1

Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency

 Maxim Greenberg , Aurélie Teissandier , Marius Walter , Daan Noordermeer , Deborah Bourc'His
eLife, 2019, 8, ⟨10.7554/eLife.44057⟩
Article dans une revue hal-03939280v1

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

 Ofir Shukron , Vincent Piras , Daan Noordermeer , David Holcman
Nature Communications, 2019, 10 (1), pp.2626. ⟨10.1038/s41467-019-10402-x⟩
Article dans une revue hal-02164120v1
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TADs and Their Borders: Free Movement or Building a Wall?

 Li-Hsin Chang , Sourav Ghosh , Daan Noordermeer
Journal of Molecular Biology, 2020, 432 (3), pp.643-652. ⟨10.1016/j.jmb.2019.11.025⟩
Article dans une revue hal-02995869v1

Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency

 Maxim Greenberg , Aurélie Teissandier , Marius Walter , Daan Noordermeer , Deborah Bourc'His
eLife, 2019, 8, ⟨10.7554/elife.44057⟩
Article dans une revue halshs-03437251v1

Enhancer loops appear stable during development and are associated with paused polymerase

 Yad Ghavi-Helm , Felix Klein , Tibor Pakozdi , Lucia Ciglar , Daan Noordermeer , et al.
Nature, 2014, 512 (7512), pp.96-100. ⟨10.1038/nature13417⟩
Article dans une revue hal-02349085v1
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3D genome organization: setting the stage and introducing its players

 Daan Noordermeer
Briefings in Functional Genomics and Proteomics, 2020, 19 (2), pp.69-70. ⟨10.1093/bfgp/elaa006⟩
Article dans une revue hal-02995866v1
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The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use

 Laura Moniot-Perron , Benoit Moindrot , Line Manceau , Joanne Edouard , Yan Jaszczyszyn , et al.
2022
Pré-publication, Document de travail hal-03818695v1

The embryonic DNA methylation program modulates the cis- regulatory landscape via CTCF antagonism

 Ana Monteagudo-Sánchez , Julien Richard Albert , Margherita Scarpa , Daan Noordermeer , Maxim V.C. Greenberg
2023
Pré-publication, Document de travail hal-04308137v1
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CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains

 David Llères , Benoît Moindrot , Rakesh Pathak , Vincent Piras , Mélody Matelot , et al.
Genome Biology, 2019, 20 (1), pp.272. ⟨10.1186/s13059-019-1896-8⟩
Article dans une revue hal-02413890v1
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Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements

 Elodie Thierion , Johan Le Men , Samuel Collombet , Céline Hernandez , Fanny Coulpier , et al.
PLoS Genetics, 2017, 13 (7), pp.e1006903. ⟨10.1371/journal.pgen.1006903⟩
Article dans une revue inserm-02158641v1
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The Drosophila Fab-7 boundary modulates Abd-B gene activity by guiding an inversion of collinear chromatin organization and alternate promoter use

 Laura Moniot-Perron , Benoit Moindrot , Line Manceau , Joanne Edouard , Yan Jaszczyszyn , et al.
Cell Reports, 2023, 42 (1), pp.111967. ⟨10.1016/j.celrep.2022.111967⟩
Article dans une revue hal-04239095v1
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A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes

 Matthieu dos Santos , Stéphanie Backer , Frédéric Auradé , Matthew Man-Kin Wong , Maud Wurmser , et al.
Nature Communications, 2022, 13 (1), pp.1039. ⟨10.1038/s41467-022-28666-1⟩
Article dans une revue pasteur-03709535v2

Large scale genomic reorganization of topological domains at the HoxD locus

 Pierre J. Fabre , Marion Leleu , Benjamin H. Mormann , Lucille Lopez-Delisle , Daan Noordermeer , et al.
Genome Biology, 2017, 18 (1), pp.149. ⟨10.1186/s13059-017-1278-z⟩
Article dans une revue hal-02281878v1
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Differential 3D chromatin organization and gene activity in genomic imprinting

 Daan Noordermeer , Robert Feil
Current Opinion in Genetics and Development, 2020, 61, pp.17-24. ⟨10.1016/j.gde.2020.03.004⟩
Article dans une revue hal-02995884v1
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RNA Pol II enters the ring of cohesin-mediated loop extrusion

 Daan Noordermeer
Nature Genetics, 2023, 55 (8), pp.1256-1258. ⟨10.1038/s41588-023-01463-2⟩
Article dans une revue hal-04239127v1
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Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina

 F. Carlier , M. Li , L. Maroc , R. Debuchy , C. Souaid , et al.
Epigenetics & Chromatin, 2021, 14 (1), ⟨10.1186/s13072-021-00395-7⟩
Article dans une revue hal-03283006v1

Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency

 Maxim van Cleef Greenberg , Aurélie Teissandier , Marius Walter , Daan Noordermeer , Deborah Bourc'His
eLife, 2019, 8, ⟨10.7554/eLife.44057⟩
Article dans une revue hal-02171009v1

Promoter–Enhancer Looping and Regulatory Neighborhoods

 Charbel Souaid , Sébastien Bloyer , Daan Noordermeer
Nuclear Architecture and Dynamics, Elsevier, pp.435--456, 2018, 978-0-12-803480-4. ⟨10.1016/B978-0-12-803480-4.00018-1⟩
Chapitre d'ouvrage hal-02183682v1
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Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

 Coline Arnould , Vincent Rocher , Thomas Clouaire , Pierre Caron , Philippe E Mangeot , et al.
2020
Pré-publication, Document de travail hal-02991048v1
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Loss of Polycomb Protein EZH2 causes major depletion of H3K27 and H3K9 tri-methylation and developmental defects in the fungus Podospora anserina

 F Carlier , R Debuchy , L Maroc , C Souaid , Daan Noordermeer , et al.
2020
Pré-publication, Document de travail hal-02991015v1
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Loop extrusion as a mechanism for formation of DNA damage repair foci

 Coline Arnould , Vincent Rocher , Anne-Laure Finoux , Thomas Clouaire , Kevin Li , et al.
Nature, 2021, 590 (7847), pp.660-665. ⟨10.1038/s41586-021-03193-z⟩
Article dans une revue hal-03385752v1

Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain.

 Maxence Vieux-Rochas , Pierre J Fabre , Marion Leleu , Denis Duboule , Daan Noordermeer
Proceedings of the National Academy of Sciences of the United States of America, 2015, pp.4672-7. ⟨10.1073/pnas.1504783112⟩
Article dans une revue hal-01464776v1
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A complex CTCF binding code defines TAD boundary structure and function

 Li-Hsin Chang , Sourav Ghosh , Andrea Papale , Mélanie Miranda , Vincent Piras , et al.
2021
Pré-publication, Document de travail hal-03420385v1

MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells

 Michal Sobecki , Charbel Souaid , Jocelyne Boulay , Vincent Guerineau , Daan Noordermeer , et al.
Cell Reports, 2018, 25 (10), pp.2891--2903.e5. ⟨10.1016/j.celrep.2018.11.027⟩
Article dans une revue hal-02183681v1

Dynamic enhancer partitioning instructs activation of a growth regulator during exit from naïve pluripotency

 Maxim V.C. Greenberg , Aurélie Teissandier , Marius Walter , Daan Noordermeer , Deborah Bourc’his
2021
Pré-publication, Document de travail halshs-03437256v1
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