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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...Loss of multilevel 3D organization during breast cancer progression Roberto Rossini1, Saleh Oshaghi1, Maxim Nekrasov2, Aurélie Bellanger3, Renae Domaschenz2, Yasmin Dijkwel2, Mohamed Abdelhalim3, Rahul Agrawal3,4, Marit Ledsaak3,4, Philippe Collas3,5, Ragnhild Eskeland3,4, David Tremethick2...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...Examining the dynamics of three-dimensional organization with multitask matrix factorization Da-Inn Lee1 and Sushmita Roy1,2 1Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA; 2Wisconsin Institute for Discovery, Madison, Wisconsin...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...Elasmobranch sequencing reveals evolutionary trends of vertebrate karyotype organization Kazuaki Yamaguchi1,6, Yoshinobu Uno1,7, Mitsutaka Kadota1, Osamu Nishimura1, Ryo Nozu2,8, Kiyomi Murakumo3, Rui Matsumoto3, Keiichi Sato2,3 and Shigehiro Kuraku1,4,5 1Laboratory for Phyloinformatics, RIKEN...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...Suv39h-catalyzed H3K9me3 is critical for euchromatic organization and the maintenance of gene transcription Christine R. Keenan1,2,4,6, Hannah D. Coughlan1,2,4, Nadia Iannarella1, Andres Tapia del Fierro1,2, Andrew Keniry1,2, Timothy M. Johanson1,2, Wing Fuk Chan1,2,7, Alexandra L. Garnham1...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...in gene clusters, a feature likely related to transcriptional control. Sparse taxon sampling and fragmentary assemblies mean that little is known about the dynamics of homeobox gene evolution across Lepidoptera or about how changes in homeobox gene number and organization relate to diversity in this large...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D Dachang Dang1, Shao-Wu Zhang1, Ran Duan2 and Shihua Zhang3,4,5,6 1Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
...Characterization of network hierarchy reflects cell state specificity in organization Jingyao Wang1,4, Yue Xue1,4, Yueying He1, Hui Quan1, Jun Zhang3 and Yi Qin Gao1,2,3 1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
....zabet@qmul.ac.ukAbstractThe DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...of meiotic folding are linked to recombination activity. We apply an integrative bioinformatics approach to analyze how three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand-break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...address: Institute of Human Genetics, Université de Montpellier, CNRS, Laboratoire de Chromatine et Biologie Cellulaire, 34094 Montpellier, France Corresponding authors: hossein.salari@ens-lyon.fr, daniel.jost@ens-lyon.frAbstractChromosome organization and dynamics are involved in regulating many...

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