skip to main content

DOE PAGESDOE PAGES

Title: The Epigenomic Landscape of Prokaryotes

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.
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [4] ;  [1] ;  [1] ;  [1] ;  [1] ;  [4] ;  [4] ;  [1] ;  [1] ;  [3] ;  [1] ;  [1] ;  [2] ;  [1] ;  [4] ;  [5]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Pacific Biosciences, Menlo Park, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
  4. New England Biolabs, Ipswich, MA (United States)
  5. Univ. of Minnesota, Minneapolis, MN (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 12; Journal Issue: 2; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
OSTI Identifier:
1379228

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., and Fang, Gang. The Epigenomic Landscape of Prokaryotes. United States: N. p., Web. doi:10.1371/journal.pgen.1005854.
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., & Fang, Gang. The Epigenomic Landscape of Prokaryotes. United States. doi:10.1371/journal.pgen.1005854.
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., and Fang, Gang. 2016. "The Epigenomic Landscape of Prokaryotes". United States. doi:10.1371/journal.pgen.1005854. https://www.osti.gov/servlets/purl/1379228.
@article{osti_1379228,
title = {The Epigenomic Landscape of Prokaryotes},
author = {Blow, Matthew J. and Clark, Tyson A. and Daum, Chris G. and Deutschbauer, Adam M. and Fomenkov, Alexey and Fries, Roxanne and Froula, Jeff and Kang, Dongwan D. and Malmstrom, Rex R. and Morgan, Richard D. and Posfai, Janos and Singh, Kanwar and Visel, Axel and Wetmore, Kelly and Zhao, Zhiying and Rubin, Edward M. and Korlach, Jonas and Pennacchio, Len A. and Roberts, Richard J. and Fang, Gang},
abstractNote = {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.},
doi = {10.1371/journal.pgen.1005854},
journal = {PLoS Genetics},
number = 2,
volume = 12,
place = {United States},
year = {2016},
month = {2}
}

Works referenced in this record:

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
journal, November 2014
  • Roberts, Richard J.; Vincze, Tamas; Posfai, Janos
  • Nucleic Acids Research, Vol. 43, Issue D1, p. D298-D299
  • DOI: 10.1093/nar/gku1046

Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009

Search and clustering orders of magnitude faster than BLAST
journal, August 2010

The COG database: an updated version includes eukaryotes
journal, January 2003
  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41