ArticleBMC bioinformatics2010
Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway.Genes · 2019Review
- DNA replication timing.Cold Spring Harbor perspectives in biology · 2013Review
- Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.Genome research · 2013Article
- The spatiotemporal program of replication in the genome of Lachancea kluyveri.Genome biology and evolution · 2013Article
- Mathematical modeling of genome replication.Physical review. E, Statistical, nonlinear, and soft matter physics · 2012Article
- Replication timing and its emergence from stochastic processes.Trends in genetics : TIG · 2012Review
- Dynamics of DNA replication in yeast.Physical review letters · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA replication is a fundamental biological process during S phase of cell division. It is initiated from several hundreds of origins along whole chromosome with different firing efficiencies (or frequency of usage). Direct measurement of origin firing efficiency by techniques such as DNA combing are time-consuming and lack the ability to measure all origins. Recent genome-wide study of DNA replication approximated origin firing efficiency by indirectly measuring other quantities related to replication. However, these approximation methods do not reflect properties of origin firing and may lead to inappropriate estimations.
resultsIn this paper, we develop a probabilistic model - Spanned Firing Time Model (SFTM) to characterize DNA replication process. The proposed model reflects current understandings about DNA replication. Origins in an individual cell may initiate replication randomly within a time window, but the population average exhibits a temporal program with some origins replicated early and the others late. By estimating DNA origin firing time and fork moving velocity from genome-wide time-course S-phase copy number variation data, we could estimate firing efficiency of all origins. The estimated firing efficiency is correlated well with the previous studies in fission and budding yeasts.
conclusionsThe new probabilistic model enables sensitive identification of origins as well as genome-wide estimation of origin firing efficiency. We have successfully estimated firing efficiencies of all origins in S. cerevisiae, S. pombe and human chromosomes 21 and 22.
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