ArticlePLoS computational biology2016
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Beyond the mean: genetic control of gene expression fidelity and dispersion.bioRxiv : the preprint server for biology · 2026Article
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- Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States.Molecular & cellular proteomics : MCP · 2025Article
- The Blueprint of Logical Decisions in a NF-κB Signaling System.ACS omega · 2024Article
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics.Nucleic acids research · 2023Article
- Anticipating response function in gene regulatory networks.Journal of the Royal Society, Interface · 2021Article
- Stochastic fluctuations in apoptotic threshold of tumour cells can enhance apoptosis and combat fractional killing.Royal Society open science · 2020Article
- Article
- The free-energy cost of interaction between DNA loops.Scientific reports · 2017Article
- Perspectives: using polymer modeling to understand the formation and function of nuclear compartments.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2017Review
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Authors and funding
3 authors.
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Abstract
According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.
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