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Regulation of DNA replication time is crucial for appropriate gene expression

ABSTRACT: Regulation of DNA replication time is crucial for appropriate gene expression

PROVIDER: PRJNA351839 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4733720_1.fastq.gz	Fastqsanger.gz
	SRR4733720_2.fastq.gz	Fastqsanger.gz
	SRR4733730_1.fastq.gz	Fastqsanger.gz
	SRR4733730_2.fastq.gz	Fastqsanger.gz
	SRR4733740_1.fastq.gz	Fastqsanger.gz

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Regulation of DNA replication time is crucial for appropriate gene expression

Project description:Eukaryotic genomes are replicated in a reproducible temporal order, however, the physiological significance is poorly understood. We compared replication dynamics in divergent yeast species and identified genomic features with conserved replication times. Histone genes were amongst the earliest replicating loci in all species. We delayed the replication of HTA1-HTB1 and discovered that this halved the histone gene expression. Finally, we show that histone and cell cycle genes in general are exempt from dosage compensation mechanisms. Thus we have uncovered one of the first physiological requirements for regulated replication time and demonstrate a direct link between replication time and gene expression.

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Project description:In eukaryotes, CDC7 kinase is crucial for DNA replication initiation and has been involved in fork processing and replication stress response. Human CDC7 requires the binding of either one of two regulatory subunits, DBF4 and DRF1, for its activity. However, it is unclear whether the two regulatory subunits target CDC7 to a specific set of substrates, thus having different biological functions, or if they act redundantly. Using genome editing technology, we generated an isogenic set of cell lines deficient in either one of the two CDC7-activating subunits: these cells are viable but present signs of genomic instability, indicating that both DBF4 and DRF1 can independently support CDC7 for bulk DNA replication. Nonetheless, DBF4-deficient cells show altered replication efficiency, including partial deficiency in MCM helicase phosphorylation and alterations in the replication timing of discrete genomic regions. Notably, we find that CDC7 function at replication forks is entirely dependent on DBF4 and not DRF1. Thus, DBF4 is the primary regulator of CDC7 activity, likely mediating most of its functions in unperturbed DNA replication and during replication fork processing upon replication interference.

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Conservation of replication timing reveals global and local regulation of replication origin activity.

Project description:DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function.

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Project description:This SuperSeries is composed of the following subset Series: GSE17229: Mouse Cells Time of Replication (ToR) GSE17235: Human Cells Time of Replication (ToR) Refer to individual Series

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