Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif.

Robin L Armstrong,Robert J Duronio,Souradip Das,Jared T Nordman,Christina A Hill

doi:10.1534/genetics.120.303155

Robin L Armstrong, Robert J Duronio + Show 3 more

Open Access

https://doi.org/10.1534/genetics.120.303155

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Abstract

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

Highlights

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT)
Our findings provide insight into the relative contributions that cell type, gene expression, cell cycle, and Rap1-interacting factor 1 (Rif1) have on RT control
By comparing genome-wide RT profiles from unperturbed cells from distinct tissues, we demonstrated that cell lineage has a larger effect on RT than Rif1, an evolutionarily conserved regulator of RT

Summary

Introduction

Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). A critical trans-acting RT-regulating factor is Rap1-interacting factor 1 (Rif1), which controls RT from yeasts to humans (Cornacchia et al 2012; Hayano et al 2012; Yamazaki et al 2012; Peace et al 2014; Foti et al 2016). In animals, it is not clear whether the genomic regions that Rif targets during differentiation are cell-type-specific or whether Rif selectively regulates specific regions of the genome regardless of cell type. The Rif1-PP1 interaction motif is required for Rif1-dependent control of RT, suggesting that PP1 recruitment to replicative helicases is the predominant mechanism Rif utilizes for RT control

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