Rif1-Dependent Control of Replication Timing

Abstract

Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the genome, DNA replication must be tightly regulated and coordinated with many other nuclear processes. These regulations, however, must also be flexible as replication kinetics can change through development and differentiation. Exactly how DNA replication is regulated and how this regulation changes through development is an active field of research. One aspect of genome duplication where much remains to be discovered is replication timing (RT), which dictates when each segment of the genome is replicated during S phase. All organisms display some level of RT, yet the precise mechanisms that govern RT remain are not fully understood. The study of Rif1, a protein that actively regulates RT from yeast to humans, provides a key to unlock the underlying molecular mechanisms controlling RT. The paradigm for Rif1 function is to delay helicase activation within certain regions of the genome, causing these regions to replicate late in S phase. Many questions, however, remain about the intricacies of Rif1 function. Here, we review the current models for the activity of Rif1 with the goal of trying to understand how Rif1 functions to establish the RT program.

The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress

“…A role of RIF1 in safeguarding the stability of replicated domains may also explain how RIF1 controls the activation of dormant origins in response to replicative stress ( Hiraga et al, 2017 ) and prevents the formation of anaphase bridges ( Hengeveld et al, 2015 ; Zaaijer et al, 2016 ). RIF1 depletion has a strong impact on replication timing ( Cornacchia et al, 2012 ; Yamazaki et al, 2012 ; Foti et al, 2016 ; Richards et al, 2022 ). The action of RIF1 on the replication timing program may result from the regulation of DDK kinase activation through RIF1 interaction with the PP1 phosphatase ( Dave et al, 2014 ; Hiraga et al, 2014 ; Mattarocci et al, 2014 ) or through its ability to bind G-quadruplexes and to organize chromatin topology ( Kanoh et al, 2015 ).…”

“…Cohesin influence origins firing locally ( Guillou et al, 2010 ), yet without determining replication timing globally ( Oldach & Nieduszynski, 2019 ), most likely via the formation of loops by extrusion ( Davidson et al, 2019 ; Kim et al, 2019 ). RIF1, a conserved protein involved in telomere capping, DNA double-strand break (DSB) repair, and chromatin organization, controls the timing of DNA replication ( Cornacchia et al, 2012 ; Hayano et al, 2012 ; Yamazaki et al, 2012 ; Foti et al, 2016 ; Mattarocci et al, 2016 ; Klein et al, 2021 ; Richards et al, 2022 ). RIF1 determines replication timing via the stabilization of chromatin architecture ( Yamazaki et al, 2013 ; Kanoh et al, 2015 ; Foti et al, 2016 ; Klein et al, 2021 ) and may regulate origin licensing owing to its interaction with PP1 phosphatase that would counteract DDK kinases ( Dave et al, 2014 ; Hiraga et al, 2014 ; Mattarocci et al, 2014 ).…”

Global early replication disrupts gene expression and chromatin conformation in a single cell cycle

“…Maintaining high rates of replication delays the normal timing of genome activation [19], but the direct role of replication in the establishment of the chromatin landscape and the transcriptionally competent state of the zygote is poorly understood [55]. This study provides new links between replication control and gene expression changes, which may be relevant to understand how key factors such as Rif1 coordinate the events of early embryonic development, through regulating both chromatin organisation and replication timing [22, 56].…”

“…Importantly the vertebrate orthologues of these factors are also rate-limiting for replication initiation during early embryonic divisions [19]. Direct recruitment and inhibition of these limiting initiation factors can also influence replication timing, for example kinetochores and the forkhead box transcription factors Fkh1/Fkh2 can drive the early firing of subsets of origins by directly recruiting Dbf4 [20, 21], while conversely Rif1 counteracts DDK activity to delay RT in late replicating domains [22].…”

DNA replication timing: Biochemical mechanisms and biological significance

“…[95] In addition, heterochromatin inhibits origin firing by Rif1-dependent recruitment of phosphatases. [45,[96][97][98][99][100][101][102][103][104] Therefore, heterochromatin's role may be to establish a zone of locally high phosphatase activity, which would counteract S-phase kinase activity and thereby reduce the probability of MCM activation. Such locally high phosphatase activity might also explain the inhibition of transcription initiation associated with heterochromatin.…”