ArticleNature communications2019
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 65 citations in OpenAlex.
- The functional organization of chromosome territories in single nuclei during zygotic genome activation.Scientific reports · 2026Article
- Improved in vivo gene knockout with high specificity using multiplexed Cas12a sgRNAs.Nature communications · 2026Article
- Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing.Genome biology and evolution · 2025Article
- From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes.Molecular biology and evolution · 2025Article
- The functional organization of chromosome territories in single nuclei during zygotic genome activation.bioRxiv : the preprint server for biology · 2025Article
- Zelda is dispensable forMolecular biology of the cell · 2025Article
- Oligopaint FISH in Drosophila Testes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Chromosome structure ineLife · 2024Article
- The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization.Nucleic acids research · 2024Article
- Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Modeling homologous chromosome recognition via nonspecific interactions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Pairtools: From sequencing data to chromosome contacts.PLoS computational biology · 2024Article
- Cooltools: Enabling high-resolution Hi-C analysis in Python.PLoS computational biology · 2024Article
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- Uncharted territories: Solving the mysteries of male meiosis in flies.PLoS genetics · 2024Review
- Transvection between nonallelic genomic positions in Drosophila.G3 (Bethesda, Md.) · 2024Article
- A Cytological F1 RNAi Screen for Defects inbioRxiv : the preprint server for biology · 2024Article
- A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH.Nature biotechnology · 2023Article
- Pairtools: from sequencing data to chromosome contacts.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
17 authors at 5 institutions in 1 country.
Funding
Abstract
Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.