Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

被引：0
作者：
Christina Kahramanoglou
Ana I. Prieto
Supriya Khedkar
Bettina Haase
Ankur Gupta
Vladimir Benes
Gillian M. Fraser
Nicholas M. Luscombe
Aswin S.N. Seshasayee
机构：
[1] University of Cambridge,Department of Pathology
[2] MRC-National Institute for Medical Research,Department of Genetics
[3] The Ridgeway,undefined
[4] Mill Hill,undefined
[5] London NW7 1AA,undefined
[6] UK.,undefined
[7] Wellcome Trust Sanger Institute,undefined
[8] Wellcome Trust Genome Campus,undefined
[9] EMBL-European Bioinformatics Institute,undefined
[10] Wellcome Trust Genome Campus,undefined
[11] National Centre for Biological Sciences,undefined
[12] Tata Institute of Fundamental Research,undefined
[13] GKVK,undefined
[14] Genomics Core Facility,undefined
[15] European Molecular Biology Laboratory,undefined
[16] Okinawa Institute of Science and Technology,undefined
[17] Tancha,undefined
[18] Onna-son,undefined
[19] Kunigami-gun,undefined
[20] Okinawa 904-0495,undefined
[21] Japan.,undefined
[22] UCL Genetics Institute,undefined
[23] Environment and Evolution,undefined
[24] University College London,undefined
[25] Cancer Research UK London Research Institute,undefined
[26] 44 Lincoln's Inn Fields,undefined
来源：
Nature Communications | / 3卷
关键词：
D O I：
暂无
中图分类号：
学科分类号：
摘要：
DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DNA at single-base resolution. Whereas most target sites (CmCWGG) are fully methylated in stationary phase cells, many sites with an extended CCmCWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. Microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor RpoS and many of its targets in stationary phase. Thus, DNA cytosine methylation is a regulator of stationary phase gene expression in E. coli.
引用
收藏
相关论文
共 145 条
  • [1] Suzuki MM(2008)DNA methylation landscapes: provocative insights from epigenomics Nat. Rev. Genet. 9 465-476
  • [2] Bird A(2002)DNA methylation in cancer: too much, but also too little Oncogene 21 5400-5413
  • [3] Ehrlich M(2011)CpG islands and the regulation of transcription Genes Dev. 25 1010-1022
  • [4] Deaton AM(1974)Bacteriophage lambda having EcoRI endonuclease sites only in the nonessential region of the genome Proc. Natl Acad. Sci. USA 71 3927-3930
  • [5] Bird A(1999)Post-segregational killing by restriction modification gene complexes: observations of individual cell deaths Biochimie 81 931-938
  • [6] Rambach A(1999)Shaping the genome—restriction-modification systems as mobile genetic elements Curr. Opin. Genet. Dev. 9 649-656
  • [7] Tiollais P(2001)Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution Nucleic Acids Res. 29 3742-3756
  • [8] Handa N(1995)Selfish behavior of restriction-modification systems Science 267 897-899
  • [9] Kobayashi I(1996)Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems J. Mol. Evol. 42 91-96
  • [10] Kobayashi I(1999)Evidence of horizontal transfer of the EcoO109I restriction-modification gene to Escherichia coli chromosomal DNA J. Bacteriol. 181 6822-6827
12345678910