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Article Dans Une Revue Nucleic Acids Research Année : 2021

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Chloé Baum
Yu-Cheng Lin
  • Fonction : Auteur
Alexey Fomenkov
Brian P Anton
Lixin Chen
  • Fonction : Auteur
Bo Yan
  • Fonction : Auteur
Thomas Evans
  • Fonction : Auteur
Andrew C Tolonen
Laurence Ettwiller

Résumé

Abstract DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and single molecule, real-time (SMRT) sequencing usually misses m5C. Here, we present a new method called RIMS-seq (rapid identification of methylase specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.

Dates et versions

hal-04167106 , version 1 (20-07-2023)

Identifiants

Citer

Chloé Baum, Yu-Cheng Lin, Alexey Fomenkov, Brian P Anton, Lixin Chen, et al.. Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes. Nucleic Acids Research, 2021, 49 (19), pp.e113-e113. ⟨10.1093/nar/gkab705⟩. ⟨hal-04167106⟩
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