Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome
15 affiliations
- 1Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- 2UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Centre for Biomedical Research and Technology, HSE University, Moscow 101000, Russia; The Center for Bio- and Medical Technologies, Moscow 121205, Russia
- 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Faculty of Informatics, Masaryk University, 601 77 Brno, Czech Republic
- 4Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- 5Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- 6UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- 7Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- 8Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- 9Coriell Institute for Medical Research, Camden, NJ 08103, USA
- 10Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA 94305, USA
- 11Department of Biochemistry, Stanford University, Palo Alto, CA 94305, USA
- 12Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
- 13Department of Anatomy and Anthropology & Department of Human Molecular Genetics and Biochemistry, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- 14Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Biohub - San Francisco, San Francisco, CA 94158, USA. Electronic address: [email protected]
- 15Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. Electronic address: [email protected]
Abstract
Centromeres ensure proper chromosome segregation during cell division, yet the organization and regulation of centromeric chromatin within satellite DNA arrays remain incompletely understood. Here, we leverage the complete diploid human genome benchmark (T2T-HG002) to provide a detailed study of centromeric sequence and chromatin architecture on individual haplotypes. Using adaptive-sampling-enriched, ultra-long-read DiMeLo-seq, we achieve single-molecule chromatin profiling across all centromeres, revealing that along single chromatin fibers, CENP-A, the histone variant specifying centromere identity, forms multiple discrete subdomains within hypomethylated centromere dip regions (CDRs) that are flanked by H3K9me3-enriched heterochromatin. Despite underlying sequence variation, CDRs localize to sequence-homogeneous domains and maintain relatively balanced CENP-A dosage and aggregate length across all chromosomes and between haplotypes. Further, we show that bidirectional changes to centromeric and pericentromeric DNA methylation are accompanied by changes to centromeric chromatin architecture. In passaged cells with centromeric hypomethylation, subdomain boundaries are eroded, and adjacent CENP-A domains tend to merge and expand. Conversely, in pluripotent stem cells with centromeric hypermethylation, CDRs are fundamentally reorganized, such that discrete hypomethylated domains are frequently consolidated into broader contiguous tracts. These methylation-associated CDR restructuring events suggest that DNA methylation acts as a principal regulator of human centromere organization, with implications for understanding centromere plasticity, epigenetic inheritance, and chromosomal instability in development and disease.
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BibTeX
@article{xu2026haplotyperesolved,
title = {{Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome}},
author = {Yuan Xu and Hailey Loucks and Julian M. Menendez and Fedor Ryabov and Julian Lucas and Monika Čechová and Luke B Morina and Emily Xu and Danilo Dubocanin and Cy Chittenden and Mobin Asri and Ivo Violich and Christian Ortiz and Joshua M.V. Gardner and Todd L. Hillaker and Sara O'Rourke and Brandy McNulty and Tamara Potapova and Matthew W. Mitchell and Jacob Price Schwartz and Aaron F. Straight and Jennifer L. Gerton and Winston Timp and Ivan A. Alexandrov and Nicolas Altemose and Karen H. Miga},
journal = {Cell Genomics},
year = {2026},
month = aug,
doi = {10.1016/j.xgen.2026.101324},
url = {https://doi.org/10.1016/j.xgen.2026.101324},
note = {CC BY},
}
RIS
TY - JOUR
TI - Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome
AU - Yuan Xu
AU - Hailey Loucks
AU - Julian M. Menendez
AU - Fedor Ryabov
AU - Julian Lucas
AU - Monika Čechová
AU - Luke B Morina
AU - Emily Xu
AU - Danilo Dubocanin
AU - Cy Chittenden
AU - Mobin Asri
AU - Ivo Violich
AU - Christian Ortiz
AU - Joshua M.V. Gardner
AU - Todd L. Hillaker
AU - Sara O'Rourke
AU - Brandy McNulty
AU - Tamara Potapova
AU - Matthew W. Mitchell
AU - Jacob Price Schwartz
AU - Aaron F. Straight
AU - Jennifer L. Gerton
AU - Winston Timp
AU - Ivan A. Alexandrov
AU - Nicolas Altemose
AU - Karen H. Miga
PY - 2026
DA - 2026/08/01
JO - Cell Genomics
DO - 10.1016/j.xgen.2026.101324
UR - https://doi.org/10.1016/j.xgen.2026.101324
AB - Centromeres ensure proper chromosome segregation during cell division, yet the organization and regulation of centromeric chromatin within satellite DNA arrays remain incompletely understood. Here, we leverage the complete diploid human genome benchmark (T2T-HG002) to provide a detailed study of centromeric sequence and chromatin architecture on individual haplotypes. Using adaptive-sampling-enriched, ultra-long-read DiMeLo-seq, we achieve single-molecule chromatin profiling across all centromeres, revealing that along single chromatin fibers, CENP-A, the histone variant specifying centromere identity, forms multiple discrete subdomains within hypomethylated centromere dip regions (CDRs) that are flanked by H3K9me3-enriched heterochromatin. Despite underlying sequence variation, CDRs localize to sequence-homogeneous domains and maintain relatively balanced CENP-A dosage and aggregate length across all chromosomes and between haplotypes. Further, we show that bidirectional changes to centromeric and pericentromeric DNA methylation are accompanied by changes to centromeric chromatin architecture. In passaged cells with centromeric hypomethylation, subdomain boundaries are eroded, and adjacent CENP-A domains tend to merge and expand. Conversely, in pluripotent stem cells with centromeric hypermethylation, CDRs are fundamentally reorganized, such that discrete hypomethylated domains are frequently consolidated into broader contiguous tracts. These methylation-associated CDR restructuring events suggest that DNA methylation acts as a principal regulator of human centromere organization, with implications for understanding centromere plasticity, epigenetic inheritance, and chromosomal instability in development and disease.
SN - 2666-979X
ER -