Extensive folding variability between homologous chromosomes in mammalian cells
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,...
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| Format: | Article |
| Language: | English |
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Springer Nature
2025-05-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/s44320-025-00107-3 |
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| author | Ibai Irastorza-Azcarate Alexander Kukalev Rieke Kempfer Christoph J Thieme Guido Mastrobuoni Julia Markowski Gesa Loof Thomas M Sparks Emily Brookes Kedar Nath Natarajan Stephan Sauer Amanda G Fisher Mario Nicodemi Bing Ren Roland F Schwarz Stefan Kempa Ana Pombo |
| author_facet | Ibai Irastorza-Azcarate Alexander Kukalev Rieke Kempfer Christoph J Thieme Guido Mastrobuoni Julia Markowski Gesa Loof Thomas M Sparks Emily Brookes Kedar Nath Natarajan Stephan Sauer Amanda G Fisher Mario Nicodemi Bing Ren Roland F Schwarz Stefan Kempa Ana Pombo |
| author_sort | Ibai Irastorza-Azcarate |
| collection | DOAJ |
| description | 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 density of single-nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer–promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression. |
| format | Article |
| id | doaj-art-9dea298ef81542c0ae40b3c20f8cdeb2 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-9dea298ef81542c0ae40b3c20f8cdeb22025-08-20T03:42:03ZengSpringer NatureMolecular Systems Biology1744-42922025-05-0121773577510.1038/s44320-025-00107-3Extensive folding variability between homologous chromosomes in mammalian cellsIbai Irastorza-Azcarate0Alexander Kukalev1Rieke Kempfer2Christoph J Thieme3Guido Mastrobuoni4Julia Markowski5Gesa Loof6Thomas M Sparks7Emily Brookes8Kedar Nath Natarajan9Stephan Sauer10Amanda G Fisher11Mario Nicodemi12Bing Ren13Roland F Schwarz14Stefan Kempa15Ana Pombo16Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Proteomics and Metabolomic PlatformMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMRC Laboratory of Medical Sciences, Imperial College LondonMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupMRC Laboratory of Medical Sciences, Imperial College LondonMRC Laboratory of Medical Sciences, Imperial College LondonDipartimento di Fisica, Università di Napoli “Federico II”, and INFNCenter for Epigenomics and Department of Cellular and Molecular Medicine, University of California, San Diego School of MedicineMax-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Evolutionary and Cancer Genomics GroupMax-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Proteomics and Metabolomic PlatformMax-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture GroupAbstract 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 density of single-nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer–promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.https://doi.org/10.1038/s44320-025-00107-3Genome StructureGene RegulationAllele-specific ExpressionPolycombHistone Locus |
| spellingShingle | Ibai Irastorza-Azcarate Alexander Kukalev Rieke Kempfer Christoph J Thieme Guido Mastrobuoni Julia Markowski Gesa Loof Thomas M Sparks Emily Brookes Kedar Nath Natarajan Stephan Sauer Amanda G Fisher Mario Nicodemi Bing Ren Roland F Schwarz Stefan Kempa Ana Pombo Extensive folding variability between homologous chromosomes in mammalian cells Molecular Systems Biology Genome Structure Gene Regulation Allele-specific Expression Polycomb Histone Locus |
| title | Extensive folding variability between homologous chromosomes in mammalian cells |
| title_full | Extensive folding variability between homologous chromosomes in mammalian cells |
| title_fullStr | Extensive folding variability between homologous chromosomes in mammalian cells |
| title_full_unstemmed | Extensive folding variability between homologous chromosomes in mammalian cells |
| title_short | Extensive folding variability between homologous chromosomes in mammalian cells |
| title_sort | extensive folding variability between homologous chromosomes in mammalian cells |
| topic | Genome Structure Gene Regulation Allele-specific Expression Polycomb Histone Locus |
| url | https://doi.org/10.1038/s44320-025-00107-3 |
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