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Article Dans Une Revue Plant Physiology Année : 2022

Epigenomic Features of DNA G-Quadruplexes and Their Roles in Regulating Rice Gene Transcription

Yilong Feng
  • Fonction : Auteur
Shentong Tao
  • Fonction : Auteur
Pengyue Zhang
  • Fonction : Auteur
  • PersonId : 1120387
Francesco Rota Sperti
  • Fonction : Auteur
Guanqing Liu
  • Fonction : Auteur
Xuejiao Cheng
  • Fonction : Auteur
Tao Zhang
Hengxiu Yu
  • Fonction : Auteur
Xiu-E Wang
  • Fonction : Auteur
Caiyan Chen
  • Fonction : Auteur
Wenli Zhang
  • Fonction : Auteur

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. 4
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Dates et versions

hal-03480348 , version 1 (14-12-2021)

Identifiants

Citer

Yilong Feng, Shentong Tao, Pengyue Zhang, Francesco Rota Sperti, Guanqing Liu, et al.. Epigenomic Features of DNA G-Quadruplexes and Their Roles in Regulating Rice Gene Transcription. Plant Physiology, 2022, 188 (3), pp.1632-1648. ⟨10.1093/plphys/kiab566⟩. ⟨hal-03480348⟩
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