G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions.

Autor: Esnault C; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Magat T; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Zine El Aabidine A; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Garcia-Oliver E; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Cucchiarini A; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France., Bouchouika S; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Lleres D; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Goerke L; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Luo Y; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France.; Université Paris-Saclay, Institut Curie, Orsay, France., Verga D; Université Paris-Saclay, Institut Curie, Orsay, France., Lacroix L; Institut de Biologie de l'École Normale Supérieure, ENS, CNRS UMR8197, Inserm U1024, Paris, France., Feil R; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France., Spicuglia S; Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France.; Equipe Labellisée Ligue Contre le Cancer, Marseille, France., Mergny JL; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau, France., Andrau JC; Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier, France. jean-christophe.andrau@igmm.cnrs.fr.
Jazyk: angličtina
Zdroj: Nature genetics [Nat Genet] 2023 Aug; Vol. 55 (8), pp. 1359-1369. Date of Electronic Publication: 2023 Jul 03.
DOI: 10.1038/s41588-023-01437-4
Abstrakt: Metazoan promoters are enriched in secondary DNA structure-forming motifs, such as G-quadruplexes (G4s). Here we describe 'G4access', an approach to isolate and sequence G4s associated with open chromatin via nuclease digestion. G4access is antibody- and crosslinking-independent and enriches for computationally predicted G4s (pG4s), most of which are confirmed in vitro. Using G4access in human and mouse cells, we identify cell-type-specific G4 enrichment correlated with nucleosome exclusion and promoter transcription. G4access allows measurement of variations in G4 repertoire usage following G4 ligand treatment, HDAC and G4 helicases inhibitors. Applying G4access to cells from reciprocal hybrid mouse crosses suggests a role for G4s in the control of active imprinting regions. Consistently, we also observed that G4access peaks are unmethylated, while methylation at pG4s correlates with nucleosome repositioning on DNA. Overall, our study provides a new tool for studying G4s in cellular dynamics and highlights their association with open chromatin, transcription and their antagonism to DNA methylation.
(© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
Externí odkaz: