Peer-Reviewed Publication
Mol Syst Biol2025;21(7):735-775.July 1, 2025Journal Article
Extensive folding variability between homologous chromosomes in mammalian cells.
Ibai Irastorza-Azcarate1, Alexander Kukalev2, Rieke Kempfer2,3,4, Christoph J Thieme2, Guido Mastrobuoni5, Julia Markowski2,3,6,7, Gesa Loof2,3,8, Thomas M Sparks2, Emily Brookes9,10, Kedar Nath Natarajan2,9,11, Stephan Sauer9,12, Amanda G Fisher9,13, Mario Nicodemi14, Bing Ren15, Roland F Schwarz6,16,17, Stefan Kempa5, Ana Pombo18,19,20,21,22
1Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany. ibai.irastorzaazcarate@mdc-berlin.de.
2Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany.
3Humboldt-Universität zu Berlin, Berlin, Germany.
4Sophia Genetics SA, A-One Park, Rolle, 1180, Switzerland.
5Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Proteomics and Metabolomic Platform, 10115, Berlin, Germany.
6Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Evolutionary and Cancer Genomics Group, 10115, Berlin, Germany.
7Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
8Aix Marseille Univ, CNRS, IBDM (UMR 7288), Turing Centre for Living Systems, Marseille, France.
9MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK.
10School of Biological Sciences, University of Southampton, Southampton, UK.
11DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
12Regeneron Ireland DAC, Dublin 2, D02 HH27, Ireland.
13Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
14Dipartimento di Fisica, Università di Napoli "Federico II", and INFN, Napoli, Italy.
15Center for Epigenomics and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
16Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Cologne, Germany.
17BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
18Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany. ana.pombo@mdc-berlin.de.
19Humboldt-Universität zu Berlin, Berlin, Germany. ana.pombo@mdc-berlin.de.
20MRC Laboratory of Medical Sciences, Imperial College London, London, W12 0NN, UK. ana.pombo@mdc-berlin.de.
21Department of Biology, Johns Hopkins University, Baltimore, MD, USA. ana.pombo@mdc-berlin.de.
22Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. ana.pombo@mdc-berlin.de.
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high den…
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