Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.21769/BioProtoc.3798 http://hdl.handle.net/11449/208911 |
Resumo: | Eukaryote nuclear genomes predominantly replicate through multiple replication origins. The number of replication origins activated per chromosome during the S-phase duration may vary according to many factors, but the predominant one is replication stress. Several studies have applied different approaches to estimate the number and map the positions of the replication origins in various organisms. However, without a parameter to restrict the minimum of necessary origins, less sensitive techniques may suggest conflicting results. The estimation of the minimum number of replication origins (MO) per chromosome is an innovative method that allows the establishment of a threshold, which serves as a parameter for genomic approaches that map origins. For this, the MO can be easily obtained through a formula that requires as parameters: chromosome size, S-phase duration, and replication rate. The chromosome size for any organism can be acquired in genomic databanks (such as NCBI), the S-phase duration can be estimated by monitoring DNA replication, and the replication rate is obtained through the DNA combing approach. The estimation of MO is a simple, quick, and easy method that provides a new methodological framework to assist studies of mapping replication origins in any organism. |
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Estimation of the Minimum Number of Replication Origins Per Chromosome in any OrganismDNA replicationReplication originsReplication rateS-phase durationChromosome sizeEukaryote nuclear genomes predominantly replicate through multiple replication origins. The number of replication origins activated per chromosome during the S-phase duration may vary according to many factors, but the predominant one is replication stress. Several studies have applied different approaches to estimate the number and map the positions of the replication origins in various organisms. However, without a parameter to restrict the minimum of necessary origins, less sensitive techniques may suggest conflicting results. The estimation of the minimum number of replication origins (MO) per chromosome is an innovative method that allows the establishment of a threshold, which serves as a parameter for genomic approaches that map origins. For this, the MO can be easily obtained through a formula that requires as parameters: chromosome size, S-phase duration, and replication rate. The chromosome size for any organism can be acquired in genomic databanks (such as NCBI), the S-phase duration can be estimated by monitoring DNA replication, and the replication rate is obtained through the DNA combing approach. The estimation of MO is a simple, quick, and easy method that provides a new methodological framework to assist studies of mapping replication origins in any organism.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Ctr Toxins Immune Response & Cell Signaling CeTIC, Butantan Inst, Cell Cycle Lab, Sao Paulo, BrazilSao Paulo State Univ UNESP, Biosci Inst, Dept Chem & Biol Sci, Botucatu, SP, BrazilSao Paulo State Univ UNESP, Biosci Inst, Dept Chem & Biol Sci, Botucatu, SP, BrazilFAPESP: 2014/24170-5FAPESP: 2017/18719-2FAPESP: 2019/10753-2FAPESP: 2020/10277-3Bio-protocolCtr Toxins Immune Response & Cell Signaling CeTICUniversidade Estadual Paulista (Unesp)Silva, Marcelo S. da [UNESP]2021-06-25T11:24:34Z2021-06-25T11:24:34Z2020-10-20info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article22http://dx.doi.org/10.21769/BioProtoc.3798Bio-protocol. Sunnyvale: Bio-protocol, v. 10, n. 20, 22 p., 2020.http://hdl.handle.net/11449/20891110.21769/BioProtoc.3798WOS:000583378300013Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBio-protocolinfo:eu-repo/semantics/openAccess2021-10-23T19:23:20Zoai:repositorio.unesp.br:11449/208911Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T19:23:20Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
title |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
spellingShingle |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism Silva, Marcelo S. da [UNESP] DNA replication Replication origins Replication rate S-phase duration Chromosome size |
title_short |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
title_full |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
title_fullStr |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
title_full_unstemmed |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
title_sort |
Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism |
author |
Silva, Marcelo S. da [UNESP] |
author_facet |
Silva, Marcelo S. da [UNESP] |
author_role |
author |
dc.contributor.none.fl_str_mv |
Ctr Toxins Immune Response & Cell Signaling CeTIC Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Silva, Marcelo S. da [UNESP] |
dc.subject.por.fl_str_mv |
DNA replication Replication origins Replication rate S-phase duration Chromosome size |
topic |
DNA replication Replication origins Replication rate S-phase duration Chromosome size |
description |
Eukaryote nuclear genomes predominantly replicate through multiple replication origins. The number of replication origins activated per chromosome during the S-phase duration may vary according to many factors, but the predominant one is replication stress. Several studies have applied different approaches to estimate the number and map the positions of the replication origins in various organisms. However, without a parameter to restrict the minimum of necessary origins, less sensitive techniques may suggest conflicting results. The estimation of the minimum number of replication origins (MO) per chromosome is an innovative method that allows the establishment of a threshold, which serves as a parameter for genomic approaches that map origins. For this, the MO can be easily obtained through a formula that requires as parameters: chromosome size, S-phase duration, and replication rate. The chromosome size for any organism can be acquired in genomic databanks (such as NCBI), the S-phase duration can be estimated by monitoring DNA replication, and the replication rate is obtained through the DNA combing approach. The estimation of MO is a simple, quick, and easy method that provides a new methodological framework to assist studies of mapping replication origins in any organism. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-10-20 2021-06-25T11:24:34Z 2021-06-25T11:24:34Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.21769/BioProtoc.3798 Bio-protocol. Sunnyvale: Bio-protocol, v. 10, n. 20, 22 p., 2020. http://hdl.handle.net/11449/208911 10.21769/BioProtoc.3798 WOS:000583378300013 |
url |
http://dx.doi.org/10.21769/BioProtoc.3798 http://hdl.handle.net/11449/208911 |
identifier_str_mv |
Bio-protocol. Sunnyvale: Bio-protocol, v. 10, n. 20, 22 p., 2020. 10.21769/BioProtoc.3798 WOS:000583378300013 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bio-protocol |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
22 |
dc.publisher.none.fl_str_mv |
Bio-protocol |
publisher.none.fl_str_mv |
Bio-protocol |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1797789955888513024 |