No abstract

1DNA replication follows a strict spatiotemporal program that intersects with chromatin structure 2 and gene regulation. However, the genetic basis of the mammalian DNA replication timing 3 program is poorly understood 1-3 . To systematically identify genetic regulators of DNA 4 replication timing, we exploited inter-individual variation in 457 human pluripotent stem cell 5 lines from 349 individuals. We show that the human genome's replication program is broadly 6 encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs 4 ) 7 -base-pair-resolution sequence determinants of replication initiation. rtQTLs function 8 individually, or in combinations of proximal and distal regulators, to affect replication timing. 9Analysis of rtQTL locations reveals a histone code for replication initiation, composed of 10 bivalent histone H3 trimethylation marks on a background of histone hyperacetylation. The H3 11 trimethylation marks are individually repressive yet synergize to promote early replication. We 12 further identify novel positive and negative regulators of DNA replication timing, the former 13 comprised of pluripotency-related transcription factors while the latter involve boundary 14 elements. Human replication timing is controlled by a multi-layered mechanism that operates 15 on target DNA sequences, is composed of dozens of effectors working combinatorially, and 16follows principles analogous to transcription regulation: a histone code, activators and 17 repressors, and a promoter-enhancer logic. 18 19Main 20Eukaryotic genomes are replicated according to a strict spatiotemporal program, in which 21 replication initiates from specific locations along chromosomes and at reproducible times. The 22

DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome’s replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) – sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation.

Background: Hepatic sortilin 1 inhibits apoB secretion and lowers plasma lipids. Results: Fish oil and fenofibrate treatments prevented fatty acid-induced hepatic Sort1 posttranslational down-regulation in Western diet-fed mice. Conclusion: Hepatic Sort1 is an in vivo target of n-3 PUFAs and fenofibrate. Significance: Increasing hepatic Sort1 by therapeutic approaches may improve plasma lipid homeostasis.

Alteration of normal ploidy (aneuploidy) can have a number of opposing effects, such as unbalancing protein abundances and inhibiting cell growth but also accelerating genetic diversification and rapid adaptation. The interplay of these detrimental and beneficial effects remains puzzling. Here, to understand how cells develop tolerance to aneuploidy, we subject disomic (i.e. with an extra chromosome copy) strains of yeast to long-term experimental evolution under strong selection, by forcing disomy maintenance and daily population dilution. We characterize mutations, karyotype alterations and gene expression changes, and dissect the associated molecular strategies. Cells with different extra chromosomes accumulated mutations at distinct rates and displayed diverse adaptive events. They tended to evolve towards normal ploidy through chromosomal DNA loss and gene expression changes. We identify genes with recurrent mutations and altered expression in multiple lines, revealing a variant that improves growth under genotoxic stresses. These findings support rapid evolvability of disomic strains that can be used to characterize fitness effects of mutations under different stress conditions.