Detection of replication origins using comparative genomics and recombinational ARS assay

Conrad A. Nieduszynski*, Anne D. Donaldson

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

Effective experimental techniques are available to identify replication origin regions in eukaryotic cells. Genome-wide identification of the precise sequence elements that direct origin activity is however still not straightforward, even in the yeast Saccharomyces cerevisiae which has the best characterised eukaryotic replication origins. The availability of genome sequences for a series of closely related (sensu stricto) budding yeasts has allowed us to take a 'comparative genomics' approach to this problem. Since they represent functional protein-binding sites, origin sequences are conserved better than the surrounding intergenic sequence within the genomes of closely related yeasts. We describe here how phylogenetic comparison data can be used to identify candidate replication origin sequences in the S. cerevisiae genome, and how large numbers of such candidate sites can simultaneously be assayed for ability to initiate replication. Similar approaches could potentially be used to identify protein-binding sequence elements having other functions, as well as replication origin sites in other species.

Original languageEnglish
Title of host publicationDNA Replication
Subtitle of host publicationMethods and Protocols
EditorsSonya Vengrova, Jacob Z Dalgaard
PublisherHumana Press
Pages295-313
Number of pages19
Volume3
ISBN (Electronic)978-1-60327-815-7
ISBN (Print)9781603278140
DOIs
Publication statusPublished - 2009

Publication series

NameMethods in Molecular Biology
Volume521
ISSN (Print)10643745

Fingerprint

Replication Origin
Genomics
Genome
Protein Binding
Saccharomyces cerevisiae
Yeasts
Intergenic DNA
Saccharomycetales
Conserved Sequence
Eukaryotic Cells
Binding Sites

Keywords

  • ARS
  • Genomic
  • Origin
  • Phylogenetic
  • Replication
  • S. cerevisiae
  • Yeast

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology

Cite this

Nieduszynski, C. A., & Donaldson, A. D. (2009). Detection of replication origins using comparative genomics and recombinational ARS assay. In S. Vengrova, & J. Z. Dalgaard (Eds.), DNA Replication: Methods and Protocols (Vol. 3, pp. 295-313). (Methods in Molecular Biology; Vol. 521). Humana Press. https://doi.org/10.1007/978-1-60327-815-7_16

Detection of replication origins using comparative genomics and recombinational ARS assay. / Nieduszynski, Conrad A.; Donaldson, Anne D.

DNA Replication: Methods and Protocols. ed. / Sonya Vengrova; Jacob Z Dalgaard. Vol. 3 Humana Press, 2009. p. 295-313 (Methods in Molecular Biology; Vol. 521).

Research output: Chapter in Book/Report/Conference proceedingChapter

Nieduszynski, CA & Donaldson, AD 2009, Detection of replication origins using comparative genomics and recombinational ARS assay. in S Vengrova & JZ Dalgaard (eds), DNA Replication: Methods and Protocols. vol. 3, Methods in Molecular Biology, vol. 521, Humana Press, pp. 295-313. https://doi.org/10.1007/978-1-60327-815-7_16
Nieduszynski CA, Donaldson AD. Detection of replication origins using comparative genomics and recombinational ARS assay. In Vengrova S, Dalgaard JZ, editors, DNA Replication: Methods and Protocols. Vol. 3. Humana Press. 2009. p. 295-313. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60327-815-7_16
Nieduszynski, Conrad A. ; Donaldson, Anne D. / Detection of replication origins using comparative genomics and recombinational ARS assay. DNA Replication: Methods and Protocols. editor / Sonya Vengrova ; Jacob Z Dalgaard. Vol. 3 Humana Press, 2009. pp. 295-313 (Methods in Molecular Biology).
@inbook{f4ce8a0d46274e4cadbf523ddd6a221a,
title = "Detection of replication origins using comparative genomics and recombinational ARS assay",
abstract = "Effective experimental techniques are available to identify replication origin regions in eukaryotic cells. Genome-wide identification of the precise sequence elements that direct origin activity is however still not straightforward, even in the yeast Saccharomyces cerevisiae which has the best characterised eukaryotic replication origins. The availability of genome sequences for a series of closely related (sensu stricto) budding yeasts has allowed us to take a 'comparative genomics' approach to this problem. Since they represent functional protein-binding sites, origin sequences are conserved better than the surrounding intergenic sequence within the genomes of closely related yeasts. We describe here how phylogenetic comparison data can be used to identify candidate replication origin sequences in the S. cerevisiae genome, and how large numbers of such candidate sites can simultaneously be assayed for ability to initiate replication. Similar approaches could potentially be used to identify protein-binding sequence elements having other functions, as well as replication origin sites in other species.",
keywords = "ARS, Genomic, Origin, Phylogenetic, Replication, S. cerevisiae, Yeast",
author = "Nieduszynski, {Conrad A.} and Donaldson, {Anne D.}",
year = "2009",
doi = "10.1007/978-1-60327-815-7_16",
language = "English",
isbn = "9781603278140",
volume = "3",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "295--313",
editor = "Sonya Vengrova and Dalgaard, {Jacob Z}",
booktitle = "DNA Replication",

}

TY - CHAP

T1 - Detection of replication origins using comparative genomics and recombinational ARS assay

AU - Nieduszynski, Conrad A.

AU - Donaldson, Anne D.

PY - 2009

Y1 - 2009

N2 - Effective experimental techniques are available to identify replication origin regions in eukaryotic cells. Genome-wide identification of the precise sequence elements that direct origin activity is however still not straightforward, even in the yeast Saccharomyces cerevisiae which has the best characterised eukaryotic replication origins. The availability of genome sequences for a series of closely related (sensu stricto) budding yeasts has allowed us to take a 'comparative genomics' approach to this problem. Since they represent functional protein-binding sites, origin sequences are conserved better than the surrounding intergenic sequence within the genomes of closely related yeasts. We describe here how phylogenetic comparison data can be used to identify candidate replication origin sequences in the S. cerevisiae genome, and how large numbers of such candidate sites can simultaneously be assayed for ability to initiate replication. Similar approaches could potentially be used to identify protein-binding sequence elements having other functions, as well as replication origin sites in other species.

AB - Effective experimental techniques are available to identify replication origin regions in eukaryotic cells. Genome-wide identification of the precise sequence elements that direct origin activity is however still not straightforward, even in the yeast Saccharomyces cerevisiae which has the best characterised eukaryotic replication origins. The availability of genome sequences for a series of closely related (sensu stricto) budding yeasts has allowed us to take a 'comparative genomics' approach to this problem. Since they represent functional protein-binding sites, origin sequences are conserved better than the surrounding intergenic sequence within the genomes of closely related yeasts. We describe here how phylogenetic comparison data can be used to identify candidate replication origin sequences in the S. cerevisiae genome, and how large numbers of such candidate sites can simultaneously be assayed for ability to initiate replication. Similar approaches could potentially be used to identify protein-binding sequence elements having other functions, as well as replication origin sites in other species.

KW - ARS

KW - Genomic

KW - Origin

KW - Phylogenetic

KW - Replication

KW - S. cerevisiae

KW - Yeast

UR - http://www.scopus.com/inward/record.url?scp=68349159310&partnerID=8YFLogxK

U2 - 10.1007/978-1-60327-815-7_16

DO - 10.1007/978-1-60327-815-7_16

M3 - Chapter

SN - 9781603278140

VL - 3

T3 - Methods in Molecular Biology

SP - 295

EP - 313

BT - DNA Replication

A2 - Vengrova, Sonya

A2 - Dalgaard, Jacob Z

PB - Humana Press

ER -