ArticleGenome research2011
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
85 citing papers in PubMed, 146 citations in OpenAlex.
- Article
- The multimerization pathway of the glucocorticoid receptor.Nucleic acids research · 2025Article
- A guide to studying 3D genome structure and dynamics in the kidney.Nature reviews. Nephrology · 2025Review
- Dose-Dependent Transcriptional Response to Ionizing Radiation Is Orchestrated with DNA Repair within the Nuclear Space.International journal of molecular sciences · 2024Article
- 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction.PLoS computational biology · 2023Article
- PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription.Nucleic acids research · 2023Article
- Long-range gene regulation in hormone-dependent cancer.Nature reviews. Cancer · 2023Review
- Emerging Epigenetic and Posttranslational Mechanisms Controlling Resistance to Glucocorticoids in Acute Lymphoblastic Leukemia.HemaSphere · 2023Review
- The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation.Science advances · 2022Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes.Life science alliance · 2021Article
- Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle.PLoS genetics · 2021Article
- Chromatin Conformation in Development and Disease.Frontiers in cell and developmental biology · 2021Review
- Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation.Communications biology · 2020Article
- Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos.Molecular cell · 2020Article
- Methods for mapping 3D chromosome architecture.Nature reviews. Genetics · 2020Review
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Multifaceted Control of GR Signaling and Its Impact on Hepatic Transcriptional Networks and Metabolism.Frontiers in endocrinology · 2020Review
- Recent advances in the spatial organization of the mammalian genome.Journal of biosciences · 2020Review
- The importance of the nuclear positioning of the PPARG gene for its expression during porcine in vitro adipogenesis.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2019Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
The spatial organization of genes in the interphase nucleus plays an important role in establishment and regulation of gene expression. Contradicting results have been reported to date, with little consensus about the dynamics of nuclear organization and the features of the contact loci. In this study, we investigated the properties and dynamics of genomic loci that are in contact with glucocorticoid receptor (GR)-responsive loci. We took a systematic approach, combining genome-wide interaction profiling by the chromosome conformation capture on chip (4C) technology with expression, protein occupancy, and chromatin accessibility profiles. This approach allowed a comprehensive analysis of how distinct features of the linear genome are organized in the three-dimensional nuclear space in the context of rapid gene regulation. We found that the transcriptional response to GR occurs without dramatic nuclear reorganization. Moreover, contrary to the view of transcription-driven organization, even genes with opposite transcriptional responses colocalize. Regions contacting GR-regulated genes are not particularly enriched for GR-regulated loci or for any functional group of genes, suggesting that these subnuclear environments are not organized to respond to a specific factor. The contact regions are, however, highly enriched for DNase I-hypersensitive sites that comprehensively mark cell-type-specific regulatory sites. These findings indicate that the nucleus is pre-organized in a conformation allowing rapid transcriptional reprogramming, and this organization is significantly correlated with cell-type-specific chromatin sites accessible to regulatory factors. Numerous open chromatin loci may be arranged in nuclear domains that are poised to respond to diverse signals in general and to permit efficient gene regulation.
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What OpenQuestion holds
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.