Chromatin Dynamics

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.

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/.