Rif1 binds to G quadruplexes and suppresses replication over long distances

Kanoh, Yutaka; Matsumoto, Seiji; Fukatsu, Rino; Kakusho, Naoko; Kono, Nobuaki; Renard-Guillet, Claire; Masuda, Koji; Iida, Keisuke; Nagasawa, Kazuo; Shirahige, Katsuhiko; Masai, Hisao

doi:10.1038/nsmb.3102

Cited by 147 publications

(176 citation statements)

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“…with multiple G4 DNA ~ Our previous studies suggested a possibility that Rif1 participates in physical interactions of distant chromatin segments, contributing to the formation of chromatin loops (6)(7)9). As shown in the previous section of this report, purified muRif1 behaves as oligomers and bears at least two G4-binding domains (NTD and CTD).…”

Section: Simultaneous Interaction Of Murif1mentioning

confidence: 89%

“…8B, column 4), but unaffected by addition of even 10-fold excess of T 6 [GA] 12 DNA (Fig. 8B, column 5).…”

Section: Simultaneous Interaction Of Murif1mentioning

confidence: 99%

“…Recently, we reported that SpRif1 specifically binds to G-quadruplex (G4) structures and regulates replication timing over a long distance (6). However, it has not been known whether G4…”

mentioning

confidence: 99%

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Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

Moriyama

Yoshizawa-Sugata

Masai

2018

Journal of Biological Chemistry

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Section: Simultaneous Interaction Of Murif1mentioning

confidence: 89%

“…8B, column 4), but unaffected by addition of even 10-fold excess of T 6 [GA] 12 DNA (Fig. 8B, column 5).…”

Section: Simultaneous Interaction Of Murif1mentioning

confidence: 99%

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Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

Moriyama

Yoshizawa-Sugata

Masai

2018

Journal of Biological Chemistry

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“…Late firing of Taz1-affected origins requires telomere-associated Rif1, which also has been implicated in DNA repair (37,38). However, Rif1 binds only a subset of Taz1-associated late origins (11,38,39), and it is conceivable that Shelterin-mediated telomeric association of these origins allows Rif1 acquisition to promote proper replication and DNA repair. In other words, Taz1-bound late origins in telomeric and arm regions might be controlled in a shared nuclear compartment.…”

Section: Discussionmentioning

confidence: 99%

Shelterin components mediate genome reorganization in response to replication stress

Mizuguchi

Taneja

Matsuda

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, highresolution, genome-wide chromosome conformation capture (Hi-C) analysis revealed prominent contacts between telomeres and chromosomal arm regions containing replication origins proximal to binding sites for Taz1, a component of the Shelterin telomere protection complex. Strikingly, we find that Shelterin components are required for interactions between Taz1-associated chromosomal arm regions and telomeres. These analyses reveal an unexpected role for Shelterin components in genome reorganization in cells experiencing replication stress, with important implications for understanding the mechanisms governing replication and genome stability.T he 3D organization of the eukaryotic genome creates specialized microenvironments that play important roles in various nuclear processes (1). In addition to regulation of gene expression, proper execution of the DNA replication program and DNA damage repair also involve dynamic organization of the genome (2, 3). Indeed, computational analyses indicate spatial segregation of replication origins based on their timing of firing during S-phase (4), suggesting that besides local chromatin structure, the 3D organization of chromosomes is an important contributing factor in the spatiotemporal control of replication (5, 6). Despite important advances, understanding the connections between diverse chromosomal events and genome organization remains an important challenge.The complexities of genome organization have been studied in several model organisms, including the fission yeast Schizosaccharomyces pombe, for which the 3D organization has been explored at high resolution (7,8). This simple eukaryote contains the basic chromosomal elements of more complex systems, including partitioning of the genome into euchromatin and heterochromatin domains. The S. pombe genome conforms to a Rabl organization pattern in which centromere clusters and telomere clusters are anchored at opposing sides of the nuclear periphery (9, 10). In addition, two key elements shape genome architecture: cohesin-dependent locally crumpled 50-to 100-kb repeating elements called "globules" on chromosome arms and the constraints imposed by the compaction of the chromatin fiber by heterochromatin domains such as at pericentromeric regions (8). The relatively small size of the S. pombe genome combined with the conserved genome...

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“…One microgram of the sheared DNA was denatured at 100°C for 10 min, and BrdUsubstituted DNA was immunoprecipitated by Dynabeads sheep-anti mouse IgG (11031; Thermo Fisher) attached to anti-BrdU antibody (MBL, MI-11-3, 2.5 μg). The beads were washed with lysis buffer and DNA was eluted, as described (50,51). The immunoprecipitated DNA was treated with proteinase K, purified by a QIAquick PCR purification kit (Qiagen), and used for quantitative PCR performed with SYBR Premix Ex Taq (TaKaRa Bio) on a LightCycler 480 (Roche).…”

Section: Methodsmentioning

confidence: 99%

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

Toteva

Mason

Kanoh

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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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

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Rif1 binds to G quadruplexes and suppresses replication over long distances

Cited by 147 publications

References 46 publications

Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

Shelterin components mediate genome reorganization in response to replication stress

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

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