ArticleProceedings of the National Academy of Sciences of the United States of America2011
Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells.Methods in molecular biology (Clifton, N.J.) · 2025Article
- H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions.Nature communications · 2021Article
- The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia.Communications biology · 2019Article
- Dense neural networks for predicting chromatin conformation.BMC bioinformatics · 2018Article
- A maximum-entropy model for predicting chromatin contacts.PLoS computational biology · 2018Article
- Towards quantitative analysis of gene regulation by enhancers.Epigenomics · 2017Review
- Chromosome-refolding model of mating-type switching in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.Genome research · 2016Article
- Architectural proteins, transcription, and the three-dimensional organization of the genome.FEBS letters · 2015Review
- Modeling chromosomes: Beyond pretty pictures.FEBS letters · 2015Review
- Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data.BMC bioinformatics · 2015Article
- Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Chromatin loops as allosteric modulators of enhancer-promoter interactions.PLoS computational biology · 2014Article
- Highly conserved ENY2/Sus1 protein binds to Drosophila CTCF and is required for barrier activity.Epigenetics · 2014Article
- Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains.Nucleic acids research · 2014Article
- Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome.PLoS genetics · 2014Article
- Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes.The EMBO journal · 2014Article
- Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function.PLoS genetics · 2013Article
- New properties of Drosophila scs and scs' insulators.PloS one · 2013Article
- Distant activation of transcription: mechanisms of enhancer action.Molecular and cellular biology · 2012Review
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Authors and funding
4 authors.
Funding
Abstract
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long-distance regulatory interactions. The mechanistic basis for insulator activity and how it relates to enhancer action-at-a-distance remains unclear. Here we explore the idea that topological loops could simultaneously account for regulatory interactions of distal enhancers and the insulating activity of boundary elements. We show that while loop formation is not in itself sufficient to explain action at a distance, incorporating transient nonspecific and moderate attractive interactions between the chromatin fibers strongly enhances long-distance regulatory interactions and is sufficient to generate a euchromatin-like state. Under these same conditions, the subdivision of the loop into two topologically independent loops by insulators inhibits interdomain interactions. The underlying cause of this effect is a suppression of crossings in the contact map at intermediate distances. Thus our model simultaneously accounts for regulatory interactions at a distance and the insulator activity of boundary elements. This unified model of the regulatory roles of chromatin loops makes several testable predictions that could be confronted with in vitro experiments, as well as genomic chromatin conformation capture and fluorescent microscopic approaches.
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