ArticleGenome biology2017
Large scale genomic reorganization of topological domains at the HoxD locus.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 32 citations in OpenAlex.
- Dbx2 regulation in limbs suggests interTAD sharing of enhancers.Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- Co-Regulated Genes and Gene Clusters.Genes · 2021Review
- The relationship between genome structure and function.Nature reviews. Genetics · 2021Review
- Homeotic Genes: Clustering, Modularity, and Diversity.Frontiers in cell and developmental biology · 2021Review
- The regulatory landscapes of developmental genes.Development (Cambridge, England) · 2020Review
- Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants.Genome medicine · 2019Article
- Tales from topographic oceans: topologically associated domains and cancer.Endocrine-related cancer · 2019Review
- Developmentally regulatedDevelopment (Cambridge, England) · 2019Article
- Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes.BMC biology · 2019Article
- Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Feather Evolution from Precocial to Altricial Birds.Zoological studies · 2019Article
- Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development.BMC biology · 2018Article
- Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus.Epigenetics & chromatin · 2018Article
- Enhancer talk.Epigenomics · 2018Review
- TheGenes & development · 2017Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts.
resultsTo assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters.
conclusionsOur results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.
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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.