ArticleBiophysical journal2011
Roles of DNA looping in enhancer-blocking activity.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
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Who cites it
5 citing papers in PubMed, 12 citations in OpenAlex.
- Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates.Nucleic acids research · 2021Article
- Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.Nucleic acids research · 2016Article
- DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.Biopolymers · 2015Article
- Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.The Journal of chemical physics · 2014Article
- Time scales in epigenetic dynamics and phenotypic heterogeneity of embryonic stem cells.PLoS computational biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancer-promoter interactions in eukaryotic genomes are often controlled by sequence elements that block the actions of enhancers. Although the experimental evidence suggests that those sequence elements contribute to forming loops of chromatin, the molecular mechanism of how such looping affects the enhancer-blocking activity is still largely unknown. In this article, the roles of DNA looping in enhancer blocking are investigated by numerically simulating the DNA conformation of a prototypical model system of gene regulation. The simulated results show that the enhancer function is indeed blocked when the enhancer is looped out so that it is separated from the promoter, which explains experimental observations of gene expression in the model system. The local structural distortion of DNA caused by looping is important for blocking, so the ability of looping to block enhancers can be lost when the loop length is much larger than the persistence length of the chain.
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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.