Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing

Abstract

Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in Burkholderia cenocepacia , an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the B. cenocepacia genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGCC sequences. Methylation motif GCGGCCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in CpG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when B. cenocepacia strains J2315 and K56-2 were compared, which suggests that GGCC methylation patterns in B. cenocepacia are strain-specific. It seems likely that 4mC methylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia .

Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data

“…While it can easily detect m4C and m6A, this technology has strong limitations to detect m5C (requires a substantial coverage rate). Therefore, performing both WGBS and SMRT sequencing can allow to determine an exhaustive methylome, something rarely done (Payelleville et al, 2018;Vandenbussche et al, 2021). (III) More recently, another longrange sequencing method, the Oxford Nanopore technology (ONT), was shown to efficiently detect modified bases.…”

Bacterial Epigenomics: Coming of Age

“…This particularly holds true for eukaryotes, where 5mC is the most common DNA modification and is associated with a variety of biological phenomena such as gene silencing, genomic imprinting, X chromosome inactivation, RNA splicing, and silencing of transposable elements ( 7 ). Perhaps due to the lower genomic predominance and anticipated minor role of 5mC in bacterial gene regulation, the use of bisulfite sequencing has been rather limited in bacteria ( 8 – 10 ). Moreover, 5mC detection by third-generation sequencing technologies has been hampered either by the need for very high sequence coverage/ten-eleven translocation dioxygenase hypermodification in SMRT-seq ( 11 ) or by the limited availability of methods to perform de novo fine mapping of methylation type and recognition motif for nanopore sequencing ( 12 ).…”