ArticlePLoS computational biology2014
Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 67 citations in OpenAlex.
- CDC20-Mediated hnRNPU Ubiquitination Regulates Chromatin Condensation and Anti-Cancer Drug Response.Cancers · 2022Article
- BRD2 compartmentalizes the accessible genome.Nature genetics · 2022Article
- Haspin kinase modulates nuclear architecture and Polycomb-dependent gene silencing.PLoS genetics · 2020Article
- Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers.Nature communications · 2019Article
- Three-dimensional organization and dynamics of the genome.Cell biology and toxicology · 2018Review
- Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells.Biochimica et biophysica acta. Gene regulatory mechanisms · 2018Article
- How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes.PLoS computational biology · 2018Article
- Nasal DNA methylation is associated with childhood asthma.Epigenomics · 2018Article
- Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Article
- Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation.Cell death & disease · 2018Article
- Identification of the elementary structural units of the DNA damage response.Nature communications · 2017Article
- Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer.Cell 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
- A Polymer Physics Investigation of the Architecture of the Murine Orthologue of theFrontiers in neuroscience · 2017Review
- Review
- Entropy gives rise to topologically associating domains.Nucleic acids research · 2016Article
- The Determinants of Directionality in Transcriptional Initiation.Trends in genetics : TIG · 2016Review
- Genome architecture: from linear organisation of chromatin to the 3D assembly in the nucleus.Chromosoma · 2016Review
- Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains.Nucleic acids research · 2016Article
- Pairing and anti-pairing: a balancing act in the diploid genome.Current opinion in genetics & development · 2016Review
Corrections and comments
- Erratum issuedCorrection: Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling.2016 · van der Wateren, Ingrid M [added]
Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control chromosome folding. Here we explore the view that intrachromosomal interactions, forming a complex pattern of loops, are a key element in chromosome folding. CTCF and cohesin are two abundant looping proteins of interphase chromosomes of higher eukaryotes. To investigate the role of looping in large-scale (supra Mb) folding of human chromosomes, we knocked down the gene that codes for CTCF and the one coding for Rad21, an essential subunit of cohesin. We measured the effect on chromosome folding using systematic 3D fluorescent in situ hybridization (FISH). Results show that chromatin becomes more compact after reducing the concentration of these two looping proteins. The molecular basis for this counter-intuitive behaviour is explored by polymer modelling usingy the Dynamic Loop model (Bohn M, Heermann DW (2010) Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5: e12218.). We show that compaction can be explained by selectively decreasing the number of short-range loops, leaving long-range looping unchanged. In support of this model prediction it has recently been shown by others that CTCF and cohesin indeed are responsible primarily for short-range looping. Our results suggest that the local and the overall changes in of chromosome structure are controlled by a delicate balance between short-range and long-range loops, allowing easy switching between, for instance, open and more compact chromatin states.
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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.