Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation.
With its noncatalytic domains, DNA-binding regions, and a catalytic core targeting the histone tails, LSD1-CoREST (lysine-specific demethylase 1; REST corepressor) is an ideal model system to study the interplay between DNA binding and histone modification in nucleosome recognition. To this end, we covalently associated LSD1-CoREST to semisynthetic nucleosomal particles. This enabled biochemical and biophysical characterizations of nucleosome binding and structural elucidation by small-angle X-ray scattering, which was extensively validated through binding assays and site-directed mutagenesis of functional interfaces. Our results suggest that LSD1-CoREST functions as an ergonomic clamp that induces the detachment of the H3 histone tail from the nucleosomal DNA to make it available for capture by the enzyme active site. The key notion emerging from these studies is the inherently competitive nature of the binding interactions because nucleosome tails, chromatin modifiers, transcription factors, and DNA represent sites for multiple and often mutually exclusive interactions.
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
Simona
S
Pilotto
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
Valentina
V
Speranzini
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
Marcello
M
Tortorici
Institut de Biologie Intégrative de la Cellule, CEA, CNRS, UPS 11, 91198 Gif-sur-Yvette, France; Université Paris-Sud 11 Bâtiment 430, 91405 Orsay, France;
Dominique
D
Durand
Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and.
Alexander
A
Fish
Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy.
Sergio
S
Valente
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
Federico
http://orcid.org/0000-0002-7818-1804
F
Forneris
Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy.
Antonello
A
Mai
Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and.
Titia K
TK
Sixma
Institut de Biologie Intégrative de la Cellule, CEA, CNRS, UPS 11, 91198 Gif-sur-Yvette, France; Université Paris-Sud 11 Bâtiment 430, 91405 Orsay, France;
Patrice
P
Vachette
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; andrea.mattevi@unipv.it.
Andrea
A
Mattevi
D020134:Catalytic Domain; D056970:Co-Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D056466:Histone Demethylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008745:Methylation; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
D056970:Co-Repressor Proteins; D006657:Histones; D009419:Nerve Tissue Proteins; D009707:Nucleosomes; C121019:RCOR1 protein, human; D004247:DNA; D056466:Histone Demethylases; C495195:KDM1A protein, human
chromatin modification; histone tails; molecular recognition; nucleosome; small-angle X-ray scattering