Epigenomic Features of DNA G-Quadruplexes and Their Roles in Regulating Rice Gene Transcription.
Fiche publication
Date publication
décembre 2021
Journal
Plant physiology
Auteurs
Membres identifiés du Cancéropôle Est :
Dr MONCHAUD David
Tous les auteurs :
Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W
Lien Pubmed
Résumé
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between TE (transposable element) and non-TE (non-transposable element) genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
Mots clés
G4, epigenomic signatures, global mapping, regulation of gene transcription, rice
Référence
Plant Physiol. 2021 Dec 6;: