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  • 1
    Publication Date: 2013-11-12
    Description: In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Yubo -- Wong, Chee-Hong -- Birnbaum, Ramon Y -- Li, Guoliang -- Favaro, Rebecca -- Ngan, Chew Yee -- Lim, Joanne -- Tai, Eunice -- Poh, Huay Mei -- Wong, Eleanor -- Mulawadi, Fabianus Hendriyan -- Sung, Wing-Kin -- Nicolis, Silvia -- Ahituv, Nadav -- Ruan, Yijun -- Wei, Chia-Lin -- 1U54HG004557-01/HG/NHGRI NIH HHS/ -- GGP12152/Telethon/Italy -- GM61390/GM/NIGMS NIH HHS/ -- R01 DK090382/DK/NIDDK NIH HHS/ -- R01 HD059862/HD/NICHD NIH HHS/ -- R01 HG004456-01/HG/NHGRI NIH HHS/ -- R01 NS079231/NS/NINDS NIH HHS/ -- R01DK090382/DK/NIDDK NIH HHS/ -- R01HD059862/HD/NICHD NIH HHS/ -- R01HG003521-01/HG/NHGRI NIH HHS/ -- R01HG005058/HG/NHGRI NIH HHS/ -- R01HG006768/HG/NHGRI NIH HHS/ -- R01NS079231/NS/NINDS NIH HHS/ -- U01 GM061390/GM/NIGMS NIH HHS/ -- U19 GM061390/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Dec 12;504(7479):306-10. doi: 10.1038/nature12716. Epub 2013 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA [2] [3] Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel (R.Y.B.); National Heart, Lung, and Blood Institute, National Institutes of Health, Systems Biology Center, 9000 Rockville Pike, Bethesda, Maryland 20892, USA (Y.Z.). ; 1] Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA [2]. ; 1] Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, UCSF, San Francisco, California 94158, USA [2] [3] Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel (R.Y.B.); National Heart, Lung, and Blood Institute, National Institutes of Health, Systems Biology Center, 9000 Rockville Pike, Bethesda, Maryland 20892, USA (Y.Z.). ; 1] The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA [2] Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore. ; Department of Biological Sciences and Biotechnology, University of Milano-Bicocca, 20126 Milano, Italy. ; Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA. ; Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore. ; Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, UCSF, San Francisco, California 94158, USA. ; The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, Connecticut 06030, USA. ; 1] Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA [2] Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24213634" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Lineage ; Chromatin/*genetics/*metabolism ; Embryonic Stem Cells/metabolism ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation/*genetics ; In Situ Hybridization, Fluorescence ; Mice ; Neural Stem Cells/metabolism ; Promoter Regions, Genetic/*genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic/genetics ; Zebrafish/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    ISSN: 0309-1651
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 316 (1993), S. 339-344 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The X-linked NFE1 gene encodes an erythroid factor involved in globin gene transcription. Using a human cDNA clone encoding this factor, we show, by in situ hybridization and by analysis of human-rodent hybrid cell lines, that this gene is located in Xp11.23. In the absence of polymorphisms in the NFE1 gene, these results allow the study of the possible relationships between NFE1 mutations and X-linked hereditary persistence of fetal hemoglobin by linkage analysis with RFLP markers of the region. A female patient, hemizygous for the NFE1 locus, shows essentially normal hematological parameters.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1434-6052
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract. We explore the phase diagram of the five-dimensional anisotropic Abelian Higgs model by Monte Carlo simulations. In particular, we study the transition between the confining phase and the four-dimensional layered Higgs phase. We find that, in a certain region of the lattice parameter space, this transition can be first order, and that each layer moves into the Higgs phase independently of the others (decoupling of layers). As the Higgs couplings vary, we find, using mean field techniques, that this transition may probably become second order.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 8
    Publication Date: 2018-01-20
    Description: Tamilarasan K. Panaliappan, Walter Wittmann, Vijay K. Jidigam, Sara Mercurio, Jessica A. Bertolini, Soufien Sghari, Raj Bose, Cedric Patthey, Silvia K. Nicolis, and Lena Gunhaga The transcription factor Sox2 is necessary to maintain pluripotency of embryonic stem cells, and to regulate neural development. Neurogenesis in the vertebrate olfactory epithelium persists from embryonic stages through adulthood. The role Sox2 plays for the development of the olfactory epithelium and neurogenesis within has, however, not been determined. Here, by analysing Sox2 conditional knockout mouse embryos and chick embryos deprived of Sox2 in the olfactory epithelium using CRISPR-Cas9, we show that Sox2 activity is crucial for the induction of the neural progenitor gene Hes5 and for subsequent differentiation of the neuronal lineage. Our results also suggest that Sox2 activity promotes the neurogenic domain in the nasal epithelium by restricting Bmp4 expression. The Sox2- deficient olfactory epithelium displays diminished cell cycle progression and proliferation, a dramatic increase in apoptosis and finally olfactory pit atrophy. Moreover, chromatin immunoprecipitation data show that Sox2 directly binds to the Hes5 promoter in both the PNS and CNS. Taken together, our results indicate that Sox2 is essential to establish, maintain and expand the neuronal progenitor pool by suppressing Bmp4 and upregulating Hes5 expression.
    Print ISSN: 0950-1991
    Electronic ISSN: 1477-9129
    Topics: Biology
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