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  • 1
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    Hox genes and H3K27me3 clustering [Developmental Biology] (2015)
    National Academy of Sciences
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    Publication Date: 2015-04-15
    Description: Embryogenesis requires the precise activation and repression of many transcriptional regulators. The Polycomb group proteins and the associated H3K27me3 histone mark are essential to maintain the inactive state of many of these genes. Mammalian Hox genes are targets of Polycomb proteins and form local 3D clusters centered on the H3K27me3...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    The dynamic architecture of Hox gene clusters (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-10-15
    Description: The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Noordermeer, Daan -- Leleu, Marion -- Splinter, Erik -- Rougemont, Jacques -- De Laat, Wouter -- Duboule, Denis -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):222-5. doi: 10.1126/science.1207194.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Research Centre Frontiers in Genetics, School of Life Sciences, Ecole Polytechnique Federale (EPFL), Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998387" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/metabolism/ultrastructure ; Embryo, Mammalian/cytology/*metabolism ; Gene Expression Regulation, Developmental ; *Genes, Homeobox ; Histones/metabolism ; Mice ; Models, Genetic ; *Multigene Family ; Transcription, Genetic ; *Transcriptional Activation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Enhancer loops appear stable during development and are associated with paused polymerase (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-07-22
    Description: Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer-promoter interactions and their dynamics during embryogenesis remain unclear. At the beta-globin locus, enhancer-promoter interactions appear dynamic and cell-type specific, whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed. The extent to which preformed enhancer-promoter conformations exist at other, more typical, loci and how transcription is eventually triggered is unclear. Here we generated a high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis, covering two developmental stages and tissue contexts, at unprecedented resolution. Although local regulatory interactions are common, long-range interactions are highly prevalent within the compact Drosophila genome. Each enhancer contacts multiple enhancers, and promoters with similar expression, suggesting a role in their co-regulation. Notably, most interactions appear unchanged between tissue context and across development, arising before gene activation, and are frequently associated with paused RNA polymerase. Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer-promoter loops through release of paused polymerase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghavi-Helm, Yad -- Klein, Felix A -- Pakozdi, Tibor -- Ciglar, Lucia -- Noordermeer, Daan -- Huber, Wolfgang -- Furlong, Eileen E M -- England -- Nature. 2014 Aug 7;512(7512):96-100. doi: 10.1038/nature13417. Epub 2014 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany. ; 1] European Molecular Biology Laboratory, Genome Biology Unit, D-69117 Heidelberg, Germany [2]. ; Swiss Federal Institute of Technology, School of Life Sciences, CH-1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043061" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Chromosomes, Insect/genetics/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Drosophila melanogaster/embryology/*enzymology/*genetics ; Embryonic Development/*genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation, Developmental/genetics ; Genetic Loci/genetics ; Genome, Insect/genetics ; Humans ; Promoter Regions, Genetic/*genetics ; Transcription Initiation, Genetic ; Transcriptional Activation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    A switch between topological domains underlies HoxD genes collinearity in mouse limbs (2013)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2013-06-08
    Description: Hox genes are major determinants of the animal body plan, where they organize structures along both the trunk and appendicular axes. During mouse limb development, Hoxd genes are transcribed in two waves: early on, when the arm and forearm are specified, and later, when digits form. The transition between early and late regulations involves a functional switch between two opposite topological domains. This switch is reflected by a subset of Hoxd genes mapping centrally into the cluster, which initially interact with the telomeric domain and subsequently swing toward the centromeric domain, where they establish new contacts. This transition between independent regulatory landscapes illustrates both the modularity of the limbs and the distinct evolutionary histories of its various pieces. It also allows the formation of an intermediate area of low HOX proteins content, which develops into the wrist, the transition between our arms and our hands. This regulatory strategy accounts for collinear Hox gene regulation in land vertebrate appendages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andrey, Guillaume -- Montavon, Thomas -- Mascrez, Benedicte -- Gonzalez, Federico -- Noordermeer, Daan -- Leleu, Marion -- Trono, Didier -- Spitz, Francois -- Duboule, Denis -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1234167. doi: 10.1126/science.1234167.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23744951" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Forelimb/*embryology ; *Gene Expression Regulation, Developmental ; *Gene Order ; *Genes, Homeobox ; *Genes, Switch ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; *Multigene Family ; Telomere/genetics ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers (2019)
    Springer Nature
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    Publication Date: 2019-06-14
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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