ArticleNature methods2023
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis.Nature protocols · 2026Review
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.Genetics · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Article
- CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci.Nature biotechnology · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- A molecular census to elucidate the demixing mechanism of membraneless organelles.Genome biology · 2025Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.bioRxiv : the preprint server for biology · 2025Article
- Three-dimensional genome structures of single mammalian sperm.Nature communications · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association.International journal of molecular sciences · 2025Article
- ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.Nature communications · 2025Article
- Basketball detection based on YOLOv8.PloS one · 2025Article
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- Article
- Evolution and function of chromatin domains across the tree of life.Nature structural & molecular biology · 2024Review
- Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and thebioRxiv : the preprint server for biology · 2024Article
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16 authors.
Funding
Abstract
Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve 'active' regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain 'inactive' regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.
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