G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions - École polytechnique Access content directly
Journal Articles Nature Genetics Year : 2023

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

Abstract

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.
Fichier principal
Vignette du fichier
13_Esnault_et_al_Nature_Genetics_2023_version_authors.pdf (28.48 Mo) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

hal-04285615 , version 1 (20-11-2023)

Licence

Attribution

Identifiers

Cite

Cyril Esnault, Talha Magat, Amal Zine El Aabidine, Encar Garcia-Oliver, Anne Cucchiarini, et al.. G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nature Genetics, 2023, 55 (8), pp.1359-1369. ⟨10.1038/s41588-023-01437-4⟩. ⟨hal-04285615⟩
20 View
0 Download

Altmetric

Share

Gmail Facebook X LinkedIn More