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| Item Type: | Preprint |
|---|---|
| Title: | Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes |
| Creators: |
Markowski, Julia  ORCID: https://orcid.org/0000-0002-0573-7832, Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Robens, Claudia ORCID: https://orcid.org/0009-0008-6712-8953, Thieme, Christoph J. ORCID: https://orcid.org/0000-0002-1566-0971, Streck, Adam ORCID: https://orcid.org/0000-0002-7302-0147, Mao, Hui, Parsi, Krishna Mohan, Maehr, René, Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288 and Schwarz, Roland F. ORCID: https://orcid.org/0000-0001-9155-4268
|
| Abstract: | Resolving the three-dimensional structure of chromatin with haplotype specificity remains a fundamental challenge for understanding genetic and epigenetic contributions to gene regulation in healthy development and in disease. Phasing of chromatin contacts derived by ligation-dependent methods relies on high single-nucleotide variant (SNV) density, which limits its applicability in human genomes where SNVs are sparse. Here, we present CoPhasing, a strategy that leverages the intrinsic haplotype fidelity of Genome Architecture Mapping (GAM), a ligation-free method that inherently captures haplotype-matched genomic neighborhoods in thin nuclear slices. CoPhasing assigns SNV-free reads to their haplotype through proximity to informative reads, enabling efficient and accurate phasing even in SNV-sparse regions. Applying CoPhasing genome-wide reveals extensive, previously inaccessible structural heterogeneity between human homologous chromosomes, demonstrating the power of GAM CoPhasing to investigate allele-specific differences in 3D genome organization and their relevance to gene regulation and disease. |
| Source: | bioRxiv |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Article Number: | 2026.06.16.732681 |
| Date: | 18 June 2026 |
| Additional Information: | Accession "GSE324313" is currently private and is scheduled to be released on Mar 01, 2027. |
| Official Publication: | https://doi.org/10.64898/2026.06.16.732681 |
| Related to: |
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