Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.

Autor: Kumar B; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden.; Epigenica AB, A Working Lab, Solna, Sweden., Navarro C; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden.; Epigenica AB, A Working Lab, Solna, Sweden., Yung PYK; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden., Lyu J; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden., Salazar Mantero A; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden., Katsori AM; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden., Schwämmle H; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden., Martin M; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden., Elsässer SJ; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden. simon.elsasser@scilifelab.se.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden. simon.elsasser@scilifelab.se.

Publikováno v: Nature protocols [Nat Protoc] 2024 Oct 03. Date of Electronic Publication: 2024 Oct 03.

Dynamic antagonism between key repressive pathways maintains the placental epigenome.

Autor: Weigert R; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Department of Medical Biotechnology, Technische Universität Berlin, Berlin, Germany., Hetzel S; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany., Bailly N; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany., Haggerty C; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany., Ilik IA; Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany., Yung PYK; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden., Navarro C; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden., Bolondi A; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany., Kumar AS; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany., Anania C; Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany., Brändl B; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany., Meierhofer D; Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany., Lupiáñez DG; Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany., Müller FJ; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.; Universitätsklinikum Schleswig-Holstein Campus Kiel, Zentrum für Integrative Psychiatrie gGmbH, Kiel, Germany., Aktas T; Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany., Elsässer SJ; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden., Kretzmer H; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany., Smith ZD; Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA. z.smith@yale.edu., Meissner A; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany. meissner@molgen.mpg.de.; Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany. meissner@molgen.mpg.de.; Broad Institute of MIT and Harvard, Cambridge, MA, USA. meissner@molgen.mpg.de.; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, US. meissner@molgen.mpg.de.

Publikováno v: Nature cell biology [Nat Cell Biol] 2023 Apr; Vol. 25 (4), pp. 579-591. Date of Electronic Publication: 2023 Apr 06.

TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation.

Autor: Stolz P; Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany., Mantero AS; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden., Tvardovskiy A; Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany., Ugur E; Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.; Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany., Wange LE; Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany., Mulholland CB; Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany., Cheng Y; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden., Wierer M; Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany., Enard W; Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany., Schneider R; Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany., Bartke T; Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany., Leonhardt H; Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany., Elsässer SJ; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden., Bultmann S; Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2022 Aug 26; Vol. 50 (15), pp. 8491-8511.

Cancer cells use self-inflicted DNA breaks to evade growth limits imposed by genotoxic stress.

Autor: Larsen BD; Biotech Research and Innovation Centre, University of Copenhagen, 2200 N Copenhagen, Denmark., Benada J; Biotech Research and Innovation Centre, University of Copenhagen, 2200 N Copenhagen, Denmark., Yung PYK; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden., Bell RAV; Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada., Pappas G; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark., Urban V; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 143 00 Prague, Czech Republic., Ahlskog JK; Biotech Research and Innovation Centre, University of Copenhagen, 2200 N Copenhagen, Denmark., Kuo TT; Biotech Research and Innovation Centre, University of Copenhagen, 2200 N Copenhagen, Denmark., Janscak P; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 143 00 Prague, Czech Republic.; Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland., Megeney LA; Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario K1H 8L6, Canada., Elsässer SJ; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden., Bartek J; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden.; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 143 00 Prague, Czech Republic., Sørensen CS; Biotech Research and Innovation Centre, University of Copenhagen, 2200 N Copenhagen, Denmark.

Publikováno v: Science (New York, N.Y.) [Science] 2022 Apr 29; Vol. 376 (6592), pp. 476-483. Date of Electronic Publication: 2022 Apr 28.

Genome-wide mapping of G-quadruplex structures with CUT&Tag.

Autor: Lyu J; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden., Shao R; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden., Kwong Yung PY; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden., Elsässer SJ; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solnavägen 9, 17165 Stockholm, Sweden.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2022 Feb 22; Vol. 50 (3), pp. e13.