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However, only a minority of LtoE-shifted contigs overlapped with S50 valleys (25%; n = 437/1,717); therefore, the differentially replicating regions upon PREP1 down-regulation are not those particularly enriched in DNA replication origins in control cells.
These thresholds should assist in replicating regions of true association.
Late replicating regions associate with the duplication hotspots, whereas deletions prevail in early replicating regions (Cardoso-Moreira and Long 2010; Cardoso-Moreira et al. 2011).
To further demonstrate SMARCA5 association with replicating regions, we used a modified ChIP assay to directly detect BrdU-labeled nascent DNA following immunoprecipitation.
Late replicating regions packed with CNEs may serve as a "testing ground" for novel genes through expression in testis or transcriptional noise (Kaessmann 2010; Polev 2012).
In humans, CNVs related with NH repair mechanisms are more frequently found in late-replicating regions, while NAHR CNVs tend to occur in early replicating regions (Koren et al., 2012).
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Loss of ORCA could be causing either changes in replication timing of late-replicating regions or the complete loss of replication of these regions.
In summary, we show that mutation rates vary within the yeast genome and correlate with replication timing such that early-replicating regions have a low mutation rate.
Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions.
Temporal Transition Regions (TTRs 22 are defined as genomic regions, several hundreds of Kb in length, that separate early- from late-replicating regions (see Methods) with reduced replication origin activity23.
Changes in heterochromatin structure due to loss of ORCA affect replication timing, preferentially at the late-replicating regions.
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