Chromatin Dynamics

Papale, Andrea, Julie Segueni, Hanae El Maroufi, Daan Noordermeer, and David Holcman. 2025. “Insulation between Adjacent TADs Is Controlled by the Width of Their Boundaries through Distinct Mechanisms.” Proceedings of the National Academy of Sciences of the United States of America 122 (11): e2413112122. https://doi.org/10.1073/pnas.2413112122.

Ghorbani, Fatemeh, Eddy N. de Boer, Michiel R. Fokkens, Jelkje de Boer-Bergsma, Corien C. Verschuuren-Bemelmans, Elles Wierenga, Hamidreza Kasaei, et al. 2024. “Identification and Copy Number Variant Analysis of Enhancer Regions of Genes Causing Spinocerebellar Ataxia.” International Journal of Molecular Sciences 25 (20): 11205. https://doi.org/10.3390/ijms252011205.

Ceppi, Ilaria, Maria Rosaria Dello Stritto, Martin Mütze, Stefan Braunshier, Valentina Mengoli, Giordano Reginato, Hồ Mỹ Phúc Võ, et al. 2024. “Mechanism of BRCA1–BARD1 Function in DNA End Resection and DNA Protection.” Nature 634 (8033): 492–500. https://doi.org/10.1038/s41586-024-07909-9.

Monteagudo-Sánchez, Ana, Julien Richard Albert, Margherita Scarpa, Daan Noordermeer, and Maxim V. C. Greenberg. 2024. “The Impact of the Embryonic DNA Methylation Program on CTCF-Mediated Genome Regulation.” Nucleic Acids Research, August, gkae724. https://doi.org/10.1093/nar/gkae724.

Chang, Li-Hsin, and Daan Noordermeer. 2024. “Permeable TAD Boundaries and Their Impact on Genome-Associated Functions.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, August, e2400137. https://doi.org/10.1002/bies.202400137.

Farhadova, Sabina, Amani Ghousein, François Charon, Caroline Surcis, Melisa Gomez-Velazques, Clara Roidor, Flavio Di Michele, et al. 2024. “The Long Non-Coding RNA Meg3 Mediates Imprinted Gene Expression during Stem Cell Differentiation.” Nucleic Acids Research, April, gkae247. https://doi.org/10.1093/nar/gkae247.

Monteagudo-Sánchez, Ana, Daan Noordermeer, and Maxim V. C. Greenberg. 2024. “The Impact of DNA Methylation on CTCF-Mediated 3D Genome Organization.” Nature Structural & Molecular Biology 31 (3): 404–12. https://doi.org/10.1038/s41594-024-01241-6.

Arnould, Coline, Vincent Rocher, Florian Saur, Aldo S. Bader, Fernando Muzzopappa, Sarah Collins, Emma Lesage, et al. 2023. “Author Correction: Chromatin Compartmentalization Regulates the Response to DNA Damage.” Nature, November. https://doi.org/10.1038/s41586-023-06841-8.

Arnould, Coline, Vincent Rocher, Florian Saur, Aldo S. Bader, Fernando Muzzopappa, Sarah Collins, Emma Lesage, et al. 2023. “Chromatin Compartmentalization Regulates the Response to DNA Damage.” Nature, October. https://doi.org/10.1038/s41586-023-06635-y.

Chang, Li-Hsin, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, et al. 2023. “Multi-Feature Clustering of CTCF Binding Creates Robustness for Loop Extrusion Blocking and Topologically Associating Domain Boundaries.” Nature Communications 14 (1): 5615. https://doi.org/10.1038/s41467-023-41265-y.

Noordermeer, Daan. 2023. “RNA Pol II Enters the Ring of Cohesin-Mediated Loop Extrusion.” Nature Genetics, July. https://doi.org/10.1038/s41588-023-01463-2.

Costa-Nunes, José A. da, and Daan Noordermeer. 2023. “TADs: Dynamic Structures to Create Stable Regulatory Functions.” Current Opinion in Structural Biology 81 (June):102622. https://doi.org/10.1016/j.sbi.2023.102622.

L, Moniot-Perron, Moindrot B, Manceau L, Edouard J, Jaszczyszyn Y, Gilardi-Hebenstreit P, Hernandez C, Bloyer S, and Noordermeer D. 2023. “The Drosophila Fab-7 Boundary Modulates Abd-B Gene Activity by Guiding an Inversion of Collinear Chromatin Organization and Alternate Promoter Use.” Cell Reports 42 (1). https://doi.org/10.1016/j.celrep.2022.111967.

Grunchec, Héloïse, Jérôme Deraze, Delphine Dardalhon-Cuménal, Valérie Ribeiro, Anne Coléno-Costes, Karine Dias, Sébastien Bloyer, Emmanuèle Mouchel-Vielh, Frédérique Peronnet, and Hélène Thomassin. 2022. “Single Amino-Acid Mutation in a Drosoph Ila Melanogaster Ribosomal Protein: An Insight in UL11 Transcriptional Activity.” PLOS ONE 17 (8): e0273198. https://doi.org/10.1371/journal.pone.0273198.

Miranda, Mélanie, Daan Noordermeer, and Benoit Moindrot. 2022. “Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-Seq.” In Spatial Genome Organization: Methods and Protocols, edited by Tom Sexton, 15–33. Methods in Molecular Biology. New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-2497-5_2.

Moindrot, Benoit, and Daan Noordermeer. 2022. “Open for Connections: HiCAR Reveals the Interactions of Accessible DNA.” Cell Genomics 2 (4): 100121. https://doi.org/10.1016/j.xgen.2022.100121.

Segueni, Julie, and Daan Noordermeer. 2022. “CTCF: A Misguided Jack-of-All-Trades in Cancer Cells.” Computational and Structural Biotechnology Journal 20 (January):2685–98. https://doi.org/10.1016/j.csbj.2022.05.044.

Carlier, F., M. Li, L. Maroc, R. Debuchy, C. Souaid, D. Noordermeer, P. Grognet, and F. Malagnac. 2021. “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.” Epigenetics & Chromatin 14 (1): 22. https://doi.org/10.1186/s13072-021-00395-7.

Arnould, Coline, Vincent Rocher, Anne-Laure Finoux, Thomas Clouaire, Kevin Li, Felix Zhou, Pierre Caron, et al. 2021. “Loop Extrusion as a Mechanism for Formation of DNA Damage Repair Foci.” Nature 590 (7847): 660–65. https://doi.org/10.1038/s41586-021-03193-z.

Chang, Li-Hsin, and Daan Noordermeer. 2020. “Of Dots and Stripes: The Morse Code of Micro-C Reveals the Ultrastructure of Transcriptional and Architectural Mammalian 3D Genome Organization.” Molecular Cell 78 (3): 376–78. https://doi.org/10.1016/j.molcel.2020.04.021.

Noordermeer, Daan, and Robert Feil. 2020. “Differential 3D Chromatin Organization and Gene Activity in Genomic Imprinting.” Current Opinion in Genetics & Development 61 (April):17–24. https://doi.org/10.1016/j.gde.2020.03.004.

Noordermeer, Daan. 2020. “3D Genome Organization: Setting the Stage and Introducing Its Players.” Briefings in Functional Genomics 19 (2): 69–70. https://doi.org/10.1093/bfgp/elaa006.

Coker, Heather, Guifeng Wei, Benoit Moindrot, Shabaz Mohammed, Tatyana Nesterova, and Neil Brockdorff. 2020. “The Role of the Xist 5’ M6A Region and RBM15 in X Chromosome Inactivation.” Wellcome Open Research 5:31. https://doi.org/10.12688/wellcomeopenres.15711.1.

Chang, Li-Hsin, Sourav Ghosh, and Daan Noordermeer. 2020. “TADs and Their Borders: Free Movement or Building a Wall?” Journal of Molecular Biology 432 (3): 643–52. https://doi.org/10.1016/j.jmb.2019.11.025.

Llères, David, Benoît Moindrot, Rakesh Pathak, Vincent Piras, Mélody Matelot, Benoît Pignard, Alice Marchand, et al. 2019. “CTCF Modulates Allele-Specific Sub-TAD Organization and Imprinted Gene Activity at the Mouse Dlk1-Dio3 and Igf2-H19 Domains.” Genome Biology 20 (1): 272. https://doi.org/10.1186/s13059-019-1896-8.

Nesterova, Tatyana B., Guifeng Wei, Heather Coker, Greta Pintacuda, Joseph S. Bowness, Tianyi Zhang, Mafalda Almeida, et al. 2019. “Systematic Allelic Analysis Defines the Interplay of Key Pathways in X Chromosome Inactivation.” Nature Communications 10 (1): 3129. https://doi.org/10.1038/s41467-019-11171-3.

Shukron, O., V. Piras, D. Noordermeer, and D. Holcman. 2019. “Statistics of Chromatin Organization during Cell Differentiation Revealed by Heterogeneous Cross-Linked Polymers.” Nature Communications 10 (1): 2626. https://doi.org/10.1038/s41467-019-10402-x.

Greenberg, Maxim Van Cleef, Aurélie Teissandier, Marius Walter, Daan Noordermeer, and Deborah Bourc’his. 2019. “Dynamic Enhancer Partitioning Instructs Activation of a Growth-Related Gene during Exit from Naïve Pluripotency.” ELife 8 (April):e44057. https://doi.org/10.7554/eLife.44057.

Sobecki, Michal, Charbel Souaid, Jocelyne Boulay, Vincent Guerineau, Daan Noordermeer, and Laure Crabbe. 2018. “MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells.” Cell Reports 25 (10): 2891-2903.e5. https://doi.org/10.1016/j.celrep.2018.11.027.

Li, Leanne, Qiqun Zeng, Arjun Bhutkar, José A. Galván, Eva Karamitopoulou, Daan Noordermeer, Mei-Wen Peng, et al. 2018. “GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth.” Cancer Cell 33 (4): 736-751.e5. https://doi.org/10.1016/j.ccell.2018.02.011.

Moindrot, Benoit, and Neil Brockdorff. 2018. “Unbiased Genetic Screen to Identify Factors Involved in X-Chromosome Inactivation Using a Pooled Bar-Coded ShRNA Library.” Methods in Molecular Biology (Clifton, N.J.) 1861:19–36. https://doi.org/10.1007/978-1-4939-8766-5_2.

Souaid, Charbel, Sébastien Bloyer, and Daan Noordermeer. 2018. “Promoter–Enhancer Looping and Regulatory Neighborhoods.” In Nuclear Architecture and Dynamics, 435–56. Elsevier. https://doi.org/10.1016/B978-0-12-803480-4.00018-1.

Fabre, Pierre J., Marion Leleu, Benjamin H. Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari, and Denis Duboule. 2017. “Large Scale Genomic Reorganization of Topological Domains at the HoxD Locus.” Genome Biology 18 (1): 149. https://doi.org/10.1186/s13059-017-1278-z.

Thierion, Elodie, Johan Le Men, Samuel Collombet, Céline Hernandez, Fanny Coulpier, Patrick Torbey, Morgane Thomas-Chollier, Daan Noordermeer, Patrick Charnay, and Pascale Gilardi-Hebenstreit. 2017. “Krox20 Hindbrain Regulation Incorporates Multiple Modes of Cooperation between Cis-Acting Elements.” PLoS Genetics 13 (7): e1006903. https://doi.org/10.1371/journal.pgen.1006903.

Pintacuda, Greta, Guifeng Wei, Chloë Roustan, Burcu Anil Kirmizitas, Nicolae Solcan, Andrea Cerase, Alfredo Castello, et al. 2017. “HnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing.” Molecular Cell 68 (5): 955-969.e10. https://doi.org/10.1016/j.molcel.2017.11.013.

Matelot, Mélody, and Daan Noordermeer. 2016. “Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-Seq).” Methods in Molecular Biology (Clifton, N.J.) 1480:223–41. https://doi.org/10.1007/978-1-4939-6380-5_20.

“Multi-Feature Clustering of CTCF Binding Creates Robustness for Loop Extrusion Blocking and Topologically Associating Domain Boundaries - PubMed.” n.d. Accessed September 13, 2023. https://pubmed.ncbi.nlm.nih.gov/37699887/.