Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

被引：151

作者：

Clausen, Anders R. ^{[1
]}

Lujan, Scott A. ^{[1
]}

Burkholder, Adam B. ^{[2
]}

Orebaugh, Clinton D. ^{[1
]}

Williams, Jessica S. ^{[1
]}

Clausen, Maryam F. ^{[3
]}

Malc, Ewa P. ^{[3
]}

Mieczkowski, Piotr A. ^{[3
]}

Fargo, David C. ^{[2
]}

Smith, Duncan J. ^{[4
]}

Kunkel, Thomas A. ^{[1
]}

机构：

[1] NIEHS, Genome Integr & Struct Biol Lab, NIH, Res Triangle Pk, NC 27709 USA

[2] NIEHS, Integrat Bioinformat, NIH, Res Triangle Pk, NC 27709 USA

[3] Univ N Carolina, Dept Genet, High Throughput Sequencing Facil, Chapel Hill, NC USA

[4] NYU, Dept Biol, Ctr Genom & Syst Biol, New York, NY 10003 USA

来源：

NATURE STRUCTURAL & MOLECULAR BIOLOGY | 2015年 / 22卷 / 03期

基金：

美国国家卫生研究院;

关键词：

DNA-POLYMERASE-EPSILON; MISMATCH REPAIR; RNASE H2; MITOCHONDRIAL; DISCRIMINATION; CONSEQUENCES; INSTABILITY; INITIATION; MUTATIONS; MECHANISM;

D O I：

10.1038/nsmb.2957

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Ribonucleotides are frequently incorporated into DNA during replication in eukaryotes. Here we map genome-wide distribution of these ribonucleotides as markers of replication enzymology in budding yeast, using a new 5' DNA end-mapping method, hydrolytic end sequencing (HydEn-seq). HydEn-seq of DNA from ribonucleotide excision repair-deficient strains reveals replicase- and strand-specific patterns of ribonucleotides in the nuclear genome. These patterns support the roles of DNA polymerases a and 8 in lagging-strand replication and of DNA polymerase w in leading-strand replication. They identify replication origins, termination zones and variations in ribonucleotide incorporation frequency across the genome that exceed three orders of magnitude. HydEn-seq also reveals strand-specific 5' DNA ends at mitochondrial replication origins, thus suggesting unidirectional replication of a circular genome. Given the conservation of enzymes that incorporate and process ribonucleotides in DNA, HydEn-seq can be used to track replication enzymology in other organisms.

引用

页码：185 / 191

页数：7

共 56 条

[51] Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases [J].

Watt, Danielle L. ;

Johansson, Erik ;

Burgers, Peter M. ;

Kunkel, Thomas A. .

DNA REPAIR, 2011, 10 (08) :897-902

[52] Ribonucleotides in DNA: Origins, repair and consequences [J].

Williams, Jessica S. ;

Kunkel, Thomas A. .

DNA REPAIR, 2014, 19 :27-37

[53] Topoisomerase 1-Mediated Removal of Ribonucleotides from Nascent Leading-Strand DNA [J].

Williams, Jessica S. ;

Smith, Dana J. ;

Marjavaara, Lisette ;

Lujan, Scott A. ;

Chabes, Andrei ;

Kunkel, Thomas A. .

MOLECULAR CELL, 2013, 49 (05) :1010-1015

[54] Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ε [J].

Williams, Jessica S. ;

Clausen, Anders R. ;

McElhinny, Stephanie A. Nick ;

Watts, Brian E. ;

Johansson, Erik ;

Kunkel, Thomas A. .

DNA REPAIR, 2012, 11 (08) :649-656

[55] Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication [J].

Yang, MY ;

Bowmaker, M ;

Reyes, A ;

Vergani, L ;

Angeli, P ;

Gringeri, E ;

Jacobs, HT ;

Holt, IJ .

CELL, 2002, 111 (04) :495-505

[56] Rescuing Stalled or Damaged Replication Forks [J].

Yeeles, Joseph T. P. ;

Poli, Jerome ;

Marians, Kenneth J. ;

Pasero, Philippe .

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 2013, 5 (05)

← 1 2 3 4 5 6 →