ArticlePLoS computational biology2014
Chromatin loops as allosteric modulators of enhancer-promoter interactions.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 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
67 citing papers in PubMed, 114 citations in OpenAlex.
- Insulators As Dynamic, Tunable Regulators of Enhancer-Promoter Coordination in LivingbioRxiv : the preprint server for biology · 2026Article
- Assessing reproducibility of Hi-C chromatin interactions using stratum-adjusted irreproducible discovery rate.Bioinformatics (Oxford, England) · 2026Article
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- 3D genetic architecture of schizophrenia risk across three neuronal subtypes.Molecular psychiatry · 2026Article
- Multi-omics investigation of perineural invasion in head and neck squamous cell carcinoma: neuroimmune mechanisms and clinical implications.Frontiers in immunology · 2026Article
- COPD-Lung Cancer Comorbidity: Mechanistic Insights and Precision Oncology Implications.International journal of chronic obstructive pulmonary disease · 2026Review
- Scale-free models of chromosome structure, dynamics, and mechanics.PNAS nexus · 2025Article
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- Endocrine Examples of Phase Separation in Biology.Endocrinology · 2025Review
- Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transcriptome, and chromatin configuration.NAR molecular medicine · 2025Article
- Barrier effects on the kinetics of cohesin-mediated loop extrusion.Biophysical journal · 2025Article
- Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation.Nature reviews. Molecular cell biology · 2024Review
- Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements.American journal of human genetics · 2024Article
- Theory of chromatin organization maintained by active loop extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications.iScience · 2023Article
- High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding.Nature communications · 2023Article
- Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes.Nature structural & molecular biology · 2022Article
- Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome.iScience · 2022Article
- BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data.Bioinformatics (Oxford, England) · 2021Article
- Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates.Nucleic acids research · 2021Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.
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.