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The Epigenomic Landscape of Prokaryotes.(Research Article)

DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylat... Full description

Journal Title: PLoS Genetics Feb 12, 2016, Vol.12(2), p.e1005854
Main Author: Blow, Matthew J.
Other Authors: Clark, Tyson A. , Daum, Chris G. , Deutschbauer, Adam M. , Fomenkov, Alexey , Fries, Roxanne , Froula, Jeff , Kang, Dongwan D. , Malmstrom, Rex R. , Morgan, Richard D. , Posfai, Janos , Singh, Kanwar , Visel, Axel , Wetmore, Kelly , Zhao, Zhiying , Rubin, Edward M. , Korlach, Jonas , Pennacchio, Len A. , Roberts, Richard J.
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
ID: ISSN: 1553-7390 ; DOI: 10.1371/journal.pgen.1005854
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recordid: gale_ofa479538943
title: The Epigenomic Landscape of Prokaryotes.(Research Article)
format: Article
creator:
  • Blow, Matthew J.
  • Clark, Tyson A.
  • Daum, Chris G.
  • Deutschbauer, Adam M.
  • Fomenkov, Alexey
  • Fries, Roxanne
  • Froula, Jeff
  • Kang, Dongwan D.
  • Malmstrom, Rex R.
  • Morgan, Richard D.
  • Posfai, Janos
  • Singh, Kanwar
  • Visel, Axel
  • Wetmore, Kelly
  • Zhao, Zhiying
  • Rubin, Edward M.
  • Korlach, Jonas
  • Pennacchio, Len A.
  • Roberts, Richard J.
subjects:
  • Genomes
  • Methylation
  • DNA Replication
  • Genes
  • Methyltransferases
  • Genomics
  • DNA
ispartof: PLoS Genetics, Feb 12, 2016, Vol.12(2), p.e1005854
description: DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
language: eng
source:
identifier: ISSN: 1553-7390 ; DOI: 10.1371/journal.pgen.1005854
fulltext: fulltext
issn:
  • 1553-7390
  • 15537390
url: Link


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titleThe Epigenomic Landscape of Prokaryotes.(Research Article)
creatorBlow, Matthew J. ; Clark, Tyson A. ; Daum, Chris G. ; Deutschbauer, Adam M. ; Fomenkov, Alexey ; Fries, Roxanne ; Froula, Jeff ; Kang, Dongwan D. ; Malmstrom, Rex R. ; Morgan, Richard D. ; Posfai, Janos ; Singh, Kanwar ; Visel, Axel ; Wetmore, Kelly ; Zhao, Zhiying ; Rubin, Edward M. ; Korlach, Jonas ; Pennacchio, Len A. ; Roberts, Richard J.
ispartofPLoS Genetics, Feb 12, 2016, Vol.12(2), p.e1005854
identifierISSN: 1553-7390 ; DOI: 10.1371/journal.pgen.1005854
subjectGenomes ; Methylation ; DNA Replication ; Genes ; Methyltransferases ; Genomics ; DNA
descriptionDNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
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titleThe Epigenomic Landscape of Prokaryotes.(Research Article)
descriptionDNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
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abstractDNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
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