An integrated view of the structure and function of the human 4D nucleome.

Autor: Dekker J; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Oksuz BA; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA., Zhang Y; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University., Wang Y; Department of Microbiology, Immunology, and Molecular Genetics; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA., Minsk MK; Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Kuang S; Gladstone Institutes, San Francisco, CA 94158., Yang L; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA., Gibcus JH; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA., Krietenstein N; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen., Rando OJ; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA., Xu J; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA., Janssens DH; Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA., Henikoff S; Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Kukalev A; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Willemin A; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Winick-Ng W; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Kempfer R; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Pombo A; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Yu M; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, La Jolla, CA, USA.; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China., Kumar P; Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Zhang L; Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Belmont AS; Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Sasaki T; San Diego Biomedical Research Institute, San Diego, CA, USA., van Schaik T; Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.; Oncode Institute, the Netherlands., Brueckner L; Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands., Peric-Hupkes D; Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.; Oncode Institute, the Netherlands., van Steensel B; Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.; Oncode Institute, the Netherlands., Wang P; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA., Chai H; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China., Kim M; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Ruan Y; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China., Zhang R; Department of Genome Sciences, University of Washington, Seattle, WA 98195., Quinodoz SA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA., Bhat P; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.; David Geffen School of Medicine at UCLA, Los Angeles, USA., Guttman M; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA., Zhao W; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Chien S; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Liu Y; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Venev SV; Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA., Plewczynski D; Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology ul. Koszykowa 75, 00-662 Warsaw, Poland.; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland., Azcarate II; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Szabó D; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Thieme CJ; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany., Szczepińska T; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115 Berlin, Germany.; Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland.; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c Street, 02-097 Warsaw, Poland., Chiliński M; Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology ul. Koszykowa 75, 00-662 Warsaw, Poland., Sengupta K; Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology ul. Koszykowa 75, 00-662 Warsaw, Poland., Conte M; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Esposito A; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Abraham A; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Zhang R; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University., Wang Y; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University., Wen X; Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA., Wu Q; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Yang Y; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University., Liu J; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Boninsegna L; Department of Microbiology, Immunology, and Molecular Genetics; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA., Yildirim A; Department of Microbiology, Immunology, and Molecular Genetics; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA., Zhan Y; Department of Microbiology, Immunology, and Molecular Genetics; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA., Chiariello AM; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Bianco S; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Lee L; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA., Hu M; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA., Li Y; Department of Biostatistics, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA., Barnett RJ; Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Cook AL; Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Emerson DJ; Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Marchal C; In silichrom Ltd, Newbury, UK., Zhao P; San Diego Biomedical Research Institute, San Diego, CA, USA., Park P; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Alver BH; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Schroeder A; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Navelkar R; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Bakker C; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Ronchetti W; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Ehmsen S; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Veit A; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Gehlenborg N; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115., Wang T; Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA., Li D; Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA., Wang X; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA.; Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China., Nicodemi M; Department of Physics, University of Naples 'Federico II', Naples, Italy; INFN, Naples, Italy., Ren B; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, La Jolla, CA, USA., Zhong S; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA., Phillips-Cremins JE; Department of Genetics, Department of Bioengineering, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA., Gilbert DM; San Diego Biomedical Research Institute, San Diego, CA, USA., Pollard KS; Gladstone Institutes, San Francisco, CA 94158., Alber F; Department of Microbiology, Immunology, and Molecular Genetics; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA., Ma J; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University., Noble WS; Department of Genome Sciences, University of Washington, Seattle, WA 98195., Yue F; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA.; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 27. Date of Electronic Publication: 2024 Oct 27.

Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.

Autor: Kocanova S; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France., Raynal F; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France., Goiffon I; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France., Oksuz BA; https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA., Baú D; Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain., Kamgoué A; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France., Cantaloube S; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France., Zhan Y; https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA., Lajoie B; https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA., Marti-Renom MA; Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain martirenom@cnag.eu.; Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Dekker J; https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA Job.Dekker@umassmed.edu.; Howard Hughes Medical Institute, Chevy Chase, MD, USA., Bystricky K; Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France kerstin.bystricky@univ-tlse3.fr.; Institut Universitaire de France (IUF), Paris, France.

Publikováno v: Life science alliance [Life Sci Alliance] 2023 Nov 21; Vol. 7 (2). Date of Electronic Publication: 2023 Nov 21 (Print Publication: 2024).

Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair.

Autor: Reid DA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;, Keegan S; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;, Leo-Macias A; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;, Watanabe G; Department of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089; and., Strande NT; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599., Chang HH; Department of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089; and., Oksuz BA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;, Fenyo D; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;, Lieber MR; Department of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089; and., Ramsden DA; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599., Rothenberg E; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; eli.rothenberg@nyumc.org.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2015 May 19; Vol. 112 (20), pp. E2575-84. Date of Electronic Publication: 2015 May 04.