Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance

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Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
 
Bertolini, Jessica A.; Favaro, Rebecca; Zhu, Yanfen; Pagin, Miriam; Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Vermunt, Marit W.; Martynoga, Ben; Barone, Cristiana; Mariani, Jessica; Cardozo, Marcos Julián; Tabanera, Noemi; Zambelli, Federico; Mercurio, Sara; Ottolenghi, Sergio; Robson, Paul; Creyghton, Menno P.; Bovolenta, Paola; Pavesi, Giulio; Guillemot, Francois; Nicolis, Silvia K.; Wei, Chia Lin
(2019) Cell Stem Cell, volume 24, issue 3, pp. 462 - 476.e6
(Article)
Abstract
Bertolini et al. report that long-range chromatin interactions in neural stem cells (NSCs) are enriched in Sox2-bound enhancers; in Sox2-deleted NSCs, interactions are reduced. Genes downregulated in Sox2-deleted cells are enriched in interactions with enhancers normally Sox2-bound. Overexpression of Socs3, a gene downregulated in mutant NSCs, rescues long-term NSC self-renewal.
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Keywords: ChIA-PET, chromatin connectivity, neural stem cells, SOX2, transcription factors, Molecular Medicine, Genetics, Cell Biology
DOI: https://doi.org/10.1016/j.stem.2019.02.004
ISSN: 1934-5909
Publisher: Cell Press
Note: Funding Information: We thank Daofeng Li and Ting Wang (Washington University, http://wang.wustl.edu/ ) for helping us host and visualize our genomic data on the WashU browser. We thank Dr. Tae-Kyung Kim for the c-fos enhancers. Research reported in this publication was supported by Telethon , AIRC , Regione Lombardia ASTIL , Fondazione Cariplo , ERANET ImprovVision ( NEURON8-Full-815-091 to S.K.N.), MINECO ( BFU2013-43213-P and BFU2016-75412-R with FEDER support), CIBERER , ISCIII , ERANET/PCIN - 2015-176-C02-01 , an Institutional Grant from Fundación Ramon Areces and Banco Santander (to P.B.), the 4DN ( U54 DK107967 ), ENCODE Consortia ( UM1 HG009409 to C.-L.W.), NCI ( P30CA034196 to C.-L.W. and C.Y.N. ), the Francis Crick Institute (which receives its core funding from Cancer Research UK; FC0010089 ), the UK Medical Research Council ( FC0010089 ), the Wellcome Trust ( FC0010089 to F.G. and B.M.), and the UK Biotechnology and Biological Sciences Research Council ( BB/K005316/1 to F.G.). J.B. was supported by short-term fellowships from EMBO and Fondazione Cariplo for two stays in Madrid. Funding Information: We thank Daofeng Li and Ting Wang (Washington University, http://wang.wustl.edu/) for helping us host and visualize our genomic data on the WashU browser. We thank Dr. Tae-Kyung Kim for the c-fos enhancers. Research reported in this publication was supported by Telethon, AIRC, Regione Lombardia ASTIL, Fondazione Cariplo, ERANET ImprovVision (NEURON8-Full-815-091 to S.K.N.), MINECO (BFU2013-43213-P and BFU2016-75412-R with FEDER support), CIBERER, ISCIII, ERANET/PCIN-2015-176-C02-01, an Institutional Grant from Fundación Ramon Areces and Banco Santander (to P.B.), the 4DN (U54 DK107967), ENCODE Consortia (UM1 HG009409 to C.-L.W.), NCI (P30CA034196 to C.-L.W. and C.Y.N.), the Francis Crick Institute (which receives its core funding from Cancer Research UK; FC0010089), the UK Medical Research Council (FC0010089), the Wellcome Trust (FC0010089 to F.G. and B.M.), and the UK Biotechnology and Biological Sciences Research Council (BB/K005316/1 to F.G.). J.B. was supported by short-term fellowships from EMBO and Fondazione Cariplo for two stays in Madrid. Publisher Copyright: © 2019 Elsevier Inc.
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