ArticleNucleic acids research2010
The three-dimensional architecture of Hox cluster silencing.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 137 citations in OpenAlex.
- A conservedRNA biology · 2023Article
- PRC2, Chromatin Regulation, and Human Disease: Insights From Molecular Structure and Function.Frontiers in oncology · 2022Review
- Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.Briefings in functional genomics · 2020Article
- Folding Keratin Gene Clusters during Skin Regional Specification.Developmental cell · 2020Article
- Characterization of GJB2 cis-regulatory elements in the DFNB1 locus.Human genetics · 2019Article
- Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types.Epigenetics & chromatin · 2019Article
- Evolutionary lability inEvolution letters · 2019Article
- Developmentally regulatedDevelopment (Cambridge, England) · 2019Article
- Molecular basis and biological function of variability in spatial genome organization.Science (New York, N.Y.) · 2019Review
- Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.Scientific reports · 2019Article
- Article
- 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.BMC genomics · 2019Article
- Challenges and guidelines toward 4D nucleome data and model standards.Nature genetics · 2018Review
- Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.eLife · 2018Article
- Novel long-range regulatory mechanisms controlling PKD2 gene expression.BMC genomics · 2018Article
- 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering.Molecular cytogenetics · 2018Review
- ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.BMC bioinformatics · 2017Article
- Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice.Nucleic acids research · 2017Article
- Reciprocal regulation of chromatin state and architecture by HOTAIRM1 contributes to temporal collinear HOXA gene activation.Nucleic acids research · 2017Article
- lncRNAs: novel players in intervertebral disc degeneration and osteoarthritis.Cell proliferation · 2017Review
1 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Spatial chromatin organization is emerging as an important mechanism to regulate the expression of genes. However, very little is known about genome architecture at high-resolution in vivo. Here, we mapped the three-dimensional organization of the human Hox clusters with chromosome conformation capture (3C) technology. We show that computational modeling of 3C data sets can identify candidate regulatory proteins of chromatin architecture and gene expression. Hox genes encode evolutionarily conserved master regulators of development which strict control has fascinated biologists for over 25 years. Proper transcriptional silencing is key to Hox function since premature expression can lead to developmental defects or human disease. We now show that the HoxA cluster is organized into multiple chromatin loops that are dependent on transcription activity. Long-range contacts were found in all four silent clusters but looping patterns were specific to each cluster. In contrast to the Drosophila homeotic bithorax complex (BX-C), we found that Polycomb proteins are only modestly required for human cluster looping and silencing. However, computational three-dimensional Hox cluster modeling identified the insulator-binding protein CTCF as a likely candidate mediating DNA loops in all clusters. Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation.
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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.