2021
DOI: 10.1101/2021.12.15.472795
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Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths

Abstract: The determinants of the locations and firing times of the multiple replication origins are still elusive in human and other metazoan organisms. Experiments can independently profile mean replication timing (MRT) and replication fork directionality (RFD) genome-wide. In the hypothesis of a constant replication fork speed, MRT and RFD are related to each other by an analytical formula so are a priori equivalent. However, we show here that experimental noises result in MRT and RFD profiles containing information … Show more

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Cited by 1 publication
(7 citation statements)
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References 84 publications
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“…[13], in which the authors synchronized cells in G1 and then measured a time course of the 3C contacts at different times after the release. To be comparable with our predictions, we compute the normalized average Micro-C contact maps around early replicating origins [40] (see Materials and Methods) (Fig. 5A and Fig.…”
Section: Resultsmentioning
confidence: 97%
See 4 more Smart Citations
“…[13], in which the authors synchronized cells in G1 and then measured a time course of the 3C contacts at different times after the release. To be comparable with our predictions, we compute the normalized average Micro-C contact maps around early replicating origins [40] (see Materials and Methods) (Fig. 5A and Fig.…”
Section: Resultsmentioning
confidence: 97%
“…To characterize the 3D organization of chromosomes during DNA replication, we introduce a thermodynamic framework that combines a 1D stochastic description of the replication process [27, 28] with a 3D polymer model of the chromosome spatio-temporal dynamics[21], including explicitly chain duplication.…”
Section: Resultsmentioning
confidence: 99%
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