DNA Replication Timing
Nicholas Rhind,David M. Gilbert +1 more
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TLDR
In this article, a correlation between replication timing and the three-dimensional structure of chromosomes has been found, which suggests that replication timing is controlled at the level of chromosomal domains, and this conclusion dovetails with parallel work on the heterogeneity of origin firing and the competition between origins for limiting activators to suggest a model in which the stochastic probability of individual origin firing is modulated by chromosomal domain structure.Abstract:
Patterns of replication within eukaryotic genomes correlate with gene expression, chromatin structure, and genome evolution Recent advances in genome-scale mapping of replication kinetics have allowed these correlations to be explored in many species, cell types, and growth conditions, and these large data sets have allowed quantitative and computational analyses One striking new correlation to emerge from these analyses is between replication timing and the three-dimensional structure of chromosomes This correlation, which is significantly stronger than with any single histone modification or chromosome-binding protein, suggests that replication timing is controlled at the level of chromosomal domains This conclusion dovetails with parallel work on the heterogeneity of origin firing and the competition between origins for limiting activators to suggest a model in which the stochastic probability of individual origin firing is modulated by chromosomal domain structure to produce patterns of replication Whether these patterns have inherent biological functions or simply reflect higher-order genome structure is an open questionread more
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References
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A three-dimensional model of the yeast genome
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TL;DR: A method to globally capture intra- and inter-chromosomal interactions is developed and applied to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae, which recapitulates known features of genome organization, thereby validating the method, and identifies new features.
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M. K. Raghuraman,Elizabeth A. Winzeler,David H. Collingwood,Sonia Y. Hunt,Lisa Wodicka,Andrew R. Conway,David J. Lockhart,Ronald W. Davis,Bonita J. Brewer,Walton L. Fangman +9 more
TL;DR: Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae, finding the two ends of each of the 16 chromosomes are highly correlated in their times of replication.
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Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
Tyrone Ryba,Ichiro Hiratani,Junjie Lu,Mari Itoh,Michael Kulik,Jinfeng Zhang,Thomas C. Schulz,Allan J. Robins,Stephen Dalton,David M. Gilbert +9 more
TL;DR: The results reveal evolutionarily conserved aspects of developmentally regulated replication programs in mammals, demonstrate the power of replication profiling to distinguish closely related cell types, and strongly support the hypothesis that replication timing domains are spatially compartmentalized structural and functional units of three-dimensional chromosomal architecture.
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Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
R. Scott Hansen,Sean Thomas,Richard Sandstrom,Theresa K. Canfield,Robert E. Thurman,Molly Weaver,Michael O. Dorschner,Stanley M. Gartler,John A. Stamatoyannopoulos +8 more
TL;DR: A genome-scale approach to map temporally ordered replicating DNA using massively parallel sequencing and applied to study regional variation in human DNA replication time across multiple human cell types revealed that DNA replication typically initiates within foci of accessible chromatin comprising clustered DNaseI hypersensitive sites, and that replication time is better correlated with chromatin accessibility than with gene expression.
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