title: Analysis of Chromatin ADP-Ribosylation at the Genome-wide Level and at Specific Loci by ADPr-ChAP.
abstract: Chromatin ADP-ribosylation regulates important cellular processes. However, the exact location and magnitude of chromatin ADP-ribosylation are largely unknown. A robust and versatile method for assessing chromatin ADP-ribosylation is therefore crucial for further understanding its function. Here, we present a chromatin affinity precipitation method based on the high specificity and avidity of two well-characterized ADP-ribose binding domains to map chromatin ADP-ribosylation at the genome-wide scale and at specific loci. Our ADPr-ChAP method revealed that in cells exposed to oxidative stress, ADP-ribosylation of chromatin scales with histone density, with highest levels at heterochromatic sites and depletion at active promoters. Furthermore, in growth factor-induced adipocyte differentiation, increased chromatin ADP-ribosylation was observed at PPARγ target genes, whose expression is ADP-ribosylation dependent. In combination with deep-sequencing and conventional chromatin immunoprecipitation, the established ADPr-ChAP provides a valuable resource for the bioinformatic comparison of ADP-ribosylation with other chromatin modifications and for addressing its role in other biologically important processes.
authors.affiliation: Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Giody
authors.initials: G
authors.lastname: Bartolomei
authors.affiliation: Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Mario
authors.initials: M
authors.lastname: Leutert
authors.affiliation: Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Manzo
authors.affiliation: Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Tuncay
authors.initials: T
authors.lastname: Baubec
authors.affiliation: Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. Electronic address: michael.hottiger@dmmd.uzh.ch.
authors.forename: Michael O
authors.initials: MO
authors.lastname: Hottiger
mesh_terms: D041721:3T3-L1 Cells; D000246:Adenosine Diphosphate Ribose / Q000378:metabolism*; D017667:Adipocytes / Q000187:drug effects / Q000378:metabolism*; D050156:Adipogenesis; D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000187:drug effects / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology; D005786:Gene Expression Regulation; D013006:Growth Hormone / Q000494:pharmacology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D006861:Hydrogen Peroxide / Q000494:pharmacology; D051379:Mice; D018384:Oxidative Stress; D047495:PPAR gamma / Q000235:genetics / Q000378:metabolism; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014162:Transfection
chemical_list: D002843:Chromatin; D047495:PPAR gamma; D000246:Adenosine Diphosphate Ribose; D013006:Growth Hormone; D006861:Hydrogen Peroxide; C499320:PARP1 protein, human; C499321:Parp1 protein, mouse; D000071137:Poly (ADP-Ribose) Polymerase-1; D011065:Poly(ADP-ribose) Polymerases