Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

Abstract

The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis-and transacting factors capable of creating heterochromatin-euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin-euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains.heterochromatin | chromatin boundaries | DNA replication program | gene silencing | fission yeast

Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation

“…Recent studies showed that it also plays important roles in DNA damage response and DNA replication timing ( 18 , 27 , 31 , 35 , 36 , 56 ). However, Rif1 has long been implicated in heterochromatin regulation in both yeast and mammalian cells ( 37 , 66 – 68 ), suggesting that it may have other conserved functions. Indeed, the Rif1 homologue from drosophila does not fully complement yeast or mammalian Rif1 function in DNA damage response ( 69 ).…”

Dependency of Heterochromatin Domains on Replication Factors

“…The new screens reported here build on our recent identification of DNA elements capable of functionally replacing the natural chromatin boundary, IR-R + , at the edge of the mating-type region ( Jakociunas et al 2013 ; Toteva et al 2017 ). IR-R + deletion leads to reduced heterochromatic silencing ( Thon et al 2002 ) that can be restored by artificial boundaries.…”

A RIF1/KAP1-based toggle switch stabilises the identities of the inactive and active X chromosomes during X inactivation

“…Another surprising finding of this work is the identification of RIF1 as a positive regulator of Xist expression. Although we have previously shown that RIF1 is associated with a number of GC-rich TSSs in mESCs 45 , most of the evidence linking RIF1 to gene expression suggests its function as a negative regulator [48][49][50][51][52] . In general, RIF1 is associated with silenced chromatin regions, raising the question of what the molecular mechanism of this positive control could be.…”

“…RIF1 is a multifaceted protein, required for the regulation of several of the nuclear processes that take place during XCI. RIF1 is the only known genome-wide regulator of replication timing [40][41][42][43][44][45][46] , it confines long-range chromatin contacts within the respective boundaries of the nuclear A/B compartments 47 and plays an as yet unclear function in the control of gene expression 45,[48][49][50][51][52] . RIF1 is an adaptor for Protein Phosphatase 1 (PP1), one of the main Ser/Thr phosphatases in eukaryotic cells 42,[53][54][55][56][57][58] .…”