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An atlas of dynamic chromatin landscapes in mouse fetal development.
Gorkin, David U; Barozzi, Iros; Zhao, Yuan; Zhang, Yanxiao; Huang, Hui; Lee, Ah Young; Li, Bin; Chiou, Joshua; Wildberg, Andre; Ding, Bo; Zhang, Bo; Wang, Mengchi; Strattan, J Seth; Davidson, Jean M; Qiu, Yunjiang; Afzal, Veena; Akiyama, Jennifer A; Plajzer-Frick, Ingrid; Novak, Catherine S; Kato, Momoe; Garvin, Tyler H; Pham, Quan T; Harrington, Anne N; Mannion, Brandon J; Lee, Elizabeth A; Fukuda-Yuzawa, Yoko; He, Yupeng; Preissl, Sebastian; Chee, Sora; Han, Jee Yun; Williams, Brian A; Trout, Diane; Amrhein, Henry; Yang, Hongbo; Cherry, J Michael; Wang, Wei; Gaulton, Kyle; Ecker, Joseph R; Shen, Yin; Dickel, Diane E; Visel, Axel; Pennacchio, Len A; Ren, Bing.
Afiliación
  • Gorkin DU; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Barozzi I; Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Zhao Y; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Zhang Y; Department of Surgery and Cancer, Imperial College London, London, UK.
  • Huang H; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Lee AY; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
  • Li B; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Chiou J; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Wildberg A; Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Ding B; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Zhang B; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Wang M; Biomedical Sciences Graduate Program, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Strattan JS; Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Davidson JM; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Qiu Y; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Afzal V; Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA.
  • Akiyama JA; Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Plajzer-Frick I; Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA.
  • Novak CS; Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA.
  • Kato M; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Garvin TH; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
  • Pham QT; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Harrington AN; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Mannion BJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Lee EA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Fukuda-Yuzawa Y; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • He Y; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Preissl S; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Chee S; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Han JY; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Williams BA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Trout D; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Amrhein H; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
  • Yang H; Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
  • Cherry JM; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Wang W; Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Gaulton K; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
  • Ecker JR; Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
  • Shen Y; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Dickel DE; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Visel A; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
  • Pennacchio LA; Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA.
  • Ren B; Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA.
Nature ; 583(7818): 744-751, 2020 07.
Article en En | MEDLINE | ID: mdl-32728240
The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Cromatina / Histonas / Secuencias Reguladoras de Ácidos Nucleicos / Desarrollo Fetal / Anotación de Secuencia Molecular / Conjuntos de Datos como Asunto Límite: Animals / Female / Humans / Male Idioma: En Revista: Nature Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Cromatina / Histonas / Secuencias Reguladoras de Ácidos Nucleicos / Desarrollo Fetal / Anotación de Secuencia Molecular / Conjuntos de Datos como Asunto Límite: Animals / Female / Humans / Male Idioma: En Revista: Nature Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos