ArticleNature communications2021
High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 46 citations in OpenAlex.
- Single-allele nanoscale mapping of regulatory variants.Nature genetics · 2026Article
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- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Using paired-end read orientations to assess technical biases in capture Hi-C.NAR genomics and bioinformatics · 2024Article
- 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.Nature structural & molecular biology · 2024Article
- Technological advances in probing 4D genome organization.Current opinion in cell biology · 2023Review
- Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.bioRxiv : the preprint server for biology · 2023Article
- New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine.Cellular & molecular immunology · 2023Review
- Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Nature methods · 2023Article
- The Mediator complex regulates enhancer-promoter interactions.Nature structural & molecular biology · 2023Article
- Information about immune cell proportions and tumor stage improves the prediction of recurrence in patients with colorectal cancer.Patterns (New York, N.Y.) · 2023Article
- A lncRNA identifieseLife · 2023Article
- Gene silencing dynamics are modulated by transiently active regulatory elements.Molecular cell · 2023Article
- Article
- Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells.Wellcome open research · 2023Article
- Tissue-specific Grb10/Ddc insulator drives allelic architecture for cardiac development.Molecular cell · 2022Article
- Distinct roles for CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction.Nature structural & molecular biology · 2022Article
- Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages.Nature communications · 2022Article
- Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.Nature protocols · 2022Review
- Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus.Nature genetics · 2021Article
Corrections and comments
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Authors and funding
19 authors at 2 institutions in 1 country.
Funding
Abstract
Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.
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Registered trials
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.