Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae
- Author:
Fu JING
1
,
2
,
3
;
Zhang JU
;
Yang LI
;
Ding NAN
;
Yue LIYA
;
Zhang XIANGLI
;
Lu DANDAN
;
Jia XINMIAO
;
Li CUIDAN
;
Guo CHONGYE
;
Yin ZHE
;
Jiang XIAOYUAN
;
Zhao YONGLIANG
;
Chen FEI
;
Zhou DONGSHENG
Author Information
1. CAS Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences and China National Center for Bioinformation,Beijing 100101,China
2. Department of Oncology,Henan Provincial People's Hospital,People's Hospital of Zhengzhou University,People's Hospital of Henan University,Zhengzhou 450001,China
3. University of Chinese Academy of Sciences,Beijing 100049,Chin
- Keywords:
DNA methylation;
Epigenomics;
6mA;
5mC;
Epigenetic regulation
- From:
Genomics, Proteomics & Bioinformatics
2022;20(2):418-434
- CountryChina
- Language:Chinese
-
Abstract:
Klebsiella pneumoniae(K.pneumoniae)is an important pathogen that can cause severe hospital-and community-acquired infections.To systematically investigate its methylation features,we determined the whole-genome sequences of 14 K.pneumoniae strains covering varying serotypes,multilocus sequence types,clonal groups,viscosity/virulence,and drug resistance.Their methy-lomes were further characterized using Pacific Biosciences single-molecule real-time and bisulfite technologies.We identified 15 methylation motifs[13 N6-methyladenine(6mA)and two 5-methylcytosine(5mC)motifs],among which eight were novel.Their corresponding DNA methyl-transferases were also validated.Additionally,we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains,and identified differential distribution pat-terns of some hemi-/un-methylated GATC motifs,which tend to be located within intergenic regions(IGRs).Specifically,we characterized the in vivo methylation kinetics at single-base resolu-tion on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation.The slow methylation of the GATC motifs in the replication origin(oriC)regions and IGRs implicates the epigenetic regulation of replication initiation and transcription.Our findings illustrate the first comprehensive dynamic methylome map of K.pneumoniae at single-base resolution,and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.
