schliessen

Filtern

 

Bibliotheken

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 methylat... Full description

Journal Title: PLoS Genetics 12 February 2016, Vol.12(2)
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 , Fang, Gang
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 1553-7404 ; E-ISSN: 1553-7404 ; DOI: 10.1371/journal.pgen.1005854
Link: https://www.osti.gov/servlets/purl/1379228
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: osti_s1379228
title: The Epigenomic Landscape of Prokaryotes
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
  • Fang, Gang
subjects:
  • Basic Biological Sciences
  • 60 Applied LIFE Sciences
  • Biology
ispartof: PLoS Genetics, 12 February 2016, Vol.12(2)
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: 1553-7404 ; E-ISSN: 1553-7404 ; DOI: 10.1371/journal.pgen.1005854
fulltext: fulltext
issn:
  • 1553-7404
  • 15537404
url: Link


@attributes
ID377194795
RANK0.07
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
LOCALfalse
PrimoNMBib
record
control
sourcerecordid1379228
sourceidosti_s
recordidTN_osti_s1379228
sourcesystemPC
dbidOTOTI
pqid1765914364
galeid479538943
display
typearticle
titleThe Epigenomic Landscape of Prokaryotes
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 ; Fang, Gang
contributorLawrence Berkeley National Lab. (Lbnl), Berkeley, Ca (United States) (Corporate Author)
ispartofPLoS Genetics, 12 February 2016, Vol.12(2)
identifier
subjectBasic Biological Sciences ; 60 Applied LIFE Sciences ; Biology
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.
languageeng
source
version10
lds50peer_reviewed
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
backlink$$Uhttps://www.osti.gov/servlets/purl/1379228$$EView_record_in_SciTech_Connect
search
creatorcontrib
0Blow, Matthew J
1Clark, Tyson A
2Daum, Chris G
3Deutschbauer, Adam M
4Fomenkov, Alexey
5Fries, Roxanne
6Froula, Jeff
7Kang, Dongwan D
8Malmstrom, Rex R
9Morgan, Richard D
10Posfai, Janos
11Singh, Kanwar
12Visel, Axel
13Wetmore, Kelly
14Zhao, Zhiying
15Rubin, Edward M
16Korlach, Jonas
17Pennacchio, Len A
18Roberts, Richard J
19Fang, Gang
titleThe Epigenomic Landscape of Prokaryotes
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.

subject
0Basic Biological Sciences
160 Applied LIFE Sciences
2Biology
general
0English
1Public Library of Science
210.1371/journal.pgen.1005854
3SciTech Connect (U.S. Dept. of Energy - Office of Scientific and Technical Information)
sourceidosti_s
recordidosti_s1379228
issn
01553-7404
115537404
rsrctypearticle
creationdate2016
addtitlePLoS Genetics
searchscope
0osti_full
1osti1
scope
0osti_full
1osti1
lsr44$$EView_record_in_SciTech_Connect
tmp01SciTech Connect (U.S. Dept. of Energy - Office of Scientific and Technical Information)
tmp02OTOTI
contributorLawrence Berkeley National Lab. (Lbnl), Berkeley, Ca (United States) (Corporate Author)
startdate20160212
enddate20160212
lsr40PLoS Genetics, 12 February 2016, Vol.12 (2)
doi10.1371/journal.pgen.1005854
citationvol 12 issue 2
lsr30VSR-Enriched:[pages, pqid, issn, galeid]
sort
titleThe Epigenomic Landscape of Prokaryotes
authorBlow, 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
creationdate20160212
lso0120160212
facets
frbrgroupid8796831461967556598
frbrtype5
newrecords20190821
languageeng
topic
0Basic Biological Sciences
160 Applied LIFE Sciences
2Biology
collectionSciTech Connect (U.S. Dept. of Energy - Office of Scientific and Technical Information)
prefilterarticles
rsrctypearticles
creatorcontrib
0Blow, Matthew J
1Clark, Tyson A
2Daum, Chris G
3Deutschbauer, Adam M
4Fomenkov, Alexey
5Fries, Roxanne
6Froula, Jeff
7Kang, Dongwan D
8Malmstrom, Rex R
9Morgan, Richard D
10Posfai, Janos
11Singh, Kanwar
12Visel, Axel
13Wetmore, Kelly
14Zhao, Zhiying
15Rubin, Edward M
16Korlach, Jonas
17Pennacchio, Len A
18Roberts, Richard J
19Fang, Gang
20Lawrence Berkeley National Lab.
jtitlePLoS Genetics
creationdate2016
toplevelpeer_reviewed
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
aulast
0Blow
1Clark
2Daum
3Deutschbauer
4Fomenkov
5Fries
6Froula
7Kang
8Malmstrom
9Morgan
10Posfai
11Singh
12Visel
13Wetmore
14Zhao
15Rubin
16Korlach
17Pennacchio
18Roberts
19Fang
20Lawrence Berkeley National Lab.
aufirst
0Matthew J
1Tyson A
2Chris G
3Adam M
4Alexey
5Roxanne
6Jeff
7Dongwan D
8Rex R
9Richard D
10Janos
11Kanwar
12Axel
13Kelly
14Zhiying
15Edward M
16Jonas
17Len A
18Richard J
19Gang
auinitM
auinit1M
au
0Blow, Matthew J
1Clark, Tyson A
2Daum, Chris G
3Deutschbauer, Adam M
4Fomenkov, Alexey
5Fries, Roxanne
6Froula, Jeff
7Kang, Dongwan D
8Malmstrom, Rex R
9Morgan, Richard D
10Posfai, Janos
11Singh, Kanwar
12Visel, Axel
13Wetmore, Kelly
14Zhao, Zhiying
15Rubin, Edward M
16Korlach, Jonas
17Pennacchio, Len A
18Roberts, Richard J
19Fang, Gang
addauLawrence Berkeley National Lab.
atitleThe Epigenomic Landscape of Prokaryotes
jtitlePLoS Genetics
risdate20160212
volume12
issue2
issn
01553-7404
115537390
eissn1553-7404
formatjournal
genrearticle
ristypeJOUR
abstract

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.

copUnited States
pubPublic Library of Science
doi10.1371/journal.pgen.1005854
oafree_for_read
pagese1005854
date2016-02-12