ArticleNucleic acids research2016
Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 53 citations in OpenAlex.
- Transcriptional regulation of human NMNAT2: insights from 3D genome sequencing and bioinformatics.The FEBS journal · 2026Article
- Review
- An enhancer RNA recruits KMT2A to regulate transcription of Myb.Cell reports · 2024Article
- MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.Nature communications · 2024Article
- An enhancer RNA recruits MLL1 to regulate transcription ofbioRxiv : the preprint server for biology · 2023Article
- Multiple lineage-specific epigenetic landscapes at the antigen receptor loci.Aging research (Hong Kong, China) · 2023Article
- Shifting landscapes: the role of 3D genomic organizations in gene regulatory strategies.Current opinion in genetics & development · 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
- Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation.Immunity · 2023Article
- Pairtools: from sequencing data to chromosome contacts.bioRxiv : the preprint server for biology · 2023Article
- Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.Trends in genetics : TIG · 2022Review
- Targeting phase separation on enhancers induced by transcription factor complex formations as a new strategy for treating drug-resistant cancers.Frontiers in oncology · 2022Review
- Enhancer redundancy in development and disease.Nature reviews. Genetics · 2021Review
- The Toolbox for Untangling Chromosome Architecture in Immune Cells.Frontiers in immunology · 2021Review
- Multi-contact 3C reveals that the human genome during interphase is largely not entangled.Nature structural & molecular biology · 2020Article
- Transcription factors: building hubs in the 3D space.Cell cycle (Georgetown, Tex.) · 2020Review
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Enhancers as regulators of antigen receptor loci three-dimensional chromatin structure.Transcription · 2020Review
- Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.Computational and structural biotechnology journal · 2020Review
- KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks.Nature cell biology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act in isolation of other interacting partners that also influence their impact. Indeed, the influence of multi-loci interactions remains something of an enigma as beyond low-resolution DNA FISH we do not have the appropriate tools to analyze these. Here we present a method that uses standard 4C-seq data to identify multi-loci interactions from the same cell. We demonstrate the feasibility of our method using 4C-seq data sets that identify known pairwise and novel tri-loci interactions involving the Tcrb and Igk antigen receptor enhancers. We further show that the three Igk enhancers, MiEκ, 3'Eκ and Edκ, interact simultaneously in this super-enhancer cluster, which add to our previous findings showing that loss of one element decreases interactions between all three elements as well as reducing their transcriptional output. These findings underscore the functional importance of simultaneous interactions and provide new insight into the relationship between enhancer elements. Our method opens the door for studying multi-loci interactions and their impact on gene regulation in other biological settings.
Indexed as
Identifiers
What OpenQuestion holds
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.