ArticleBiophysical journal2010
Histone depletion facilitates chromatin loops on the kilobasepair scale.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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
22 citing papers in PubMed, 40 citations in OpenAlex.
- The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Chromatin transitions triggered by LH density as epigenetic regulators of the genome.Nucleic acids research · 2022Article
- Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.Life (Basel, Switzerland) · 2022Article
- Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks.Biophysical journal · 2020Article
- Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.Biophysical journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Novel insights into chromosomal conformations in cancer.Molecular cancer · 2017Review
- Towards quantitative analysis of gene regulation by enhancers.Epigenomics · 2017Review
- Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion.The journal of physical chemistry. B · 2017Article
- Nucleosome-free DNA regions differentially affect distant communication in chromatin.Nucleic acids research · 2017Article
- Contributions of Sequence to the Higher-Order Structures of DNA.Biophysical journal · 2017Review
- Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure.PLoS computational biology · 2017Article
- Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure.PLoS computational biology · 2016Article
- Changing chromatin fiber conformation by nucleosome repositioning.Biophysical journal · 2014Article
- The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis.The Plant cell · 2014Article
- Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator.Nucleic acids research · 2013Article
- Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.The Journal of biological chemistry · 2012Article
- The post-mitotic state in neurons correlates with a stable nuclear higher-order structure.Communicative & integrative biology · 2012Article
- Salt-modulated structure of polyelectrolyte-macroion complex fibers.The European physical journal. E, Soft matter · 2011Article
- Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations.BMC biophysics · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The packing of eukaryotic DNA in the nucleus is decisive for its function; for instance, contact between remote genome sites constitutes a basic feature of gene regulation. Interactions among regulatory proteins, DNA binding, and transcription activation are facilitated by looping of the intervening chromatin. Such long-range interactions depend on the bending flexibility of chromatin, i.e., the ring-closure probability is a directly measurable indicator of polymer flexibility. The applicability of a wormlike chain model to naked DNA has been widely accepted. However, whether this model also suffices to describe the flexibility of eukaryotic interphase chromatin is still a matter of discussion. Here we compare both 5C data from a gene desert and data from fluorescence in situ hybridization with the results of a Monte Carlo simulation of chromatin fibers with and without histone depletion. We then estimate the ring-closure probabilities of simulated fibers with estimates from analytical calculations and show that the wormlike chain model grossly underestimates chromatin flexibility for sharp bends. Most importantly, we find that only fibers with random depletion of linker histones or nucleosomes can explain the probability of random chromatin contacts on small length scales that play an important role in gene regulation. It is possible that missing linker histones and nucleosomes are not just simple, unavoidable, randomly occurring defects, but instead play a regulatory role in gene expression.
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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.