Rif1 promotes association of G-quadruplex (G4) by its specific G4 binding and oligomerization activities

Abstract

Rif1 is a conserved protein regulating replication timing and binds preferentially to the vicinity of late-firing/dormant origins in fission yeast. The Rif1 binding sites on the fission yeast genome have an intrinsic potential to generate G-quadruplex (G4) structures to which purified Rif1 preferentially binds. We previously proposed that Rif1 generates chromatin architecture that may determine replication timing by facilitating the chromatin loop formation. Here, we conducted detailed biochemical analyses on Rif1 and its G4 binding. Rif1 prefers sequences containing long stretches of guanines and binds preferentially to the multimeric G4 of parallel or hybrid/mix topology. Rif1 forms oligomers and binds simultaneously to multiple G4. We present a model on how Rif1 may facilitate the formation of chromatin architecture through its G4 binding and oligomerization properties.

Heterochromatin replication goes hand in hand with telomere protection

“…In budding and fission yeasts, only a subset of the Rif1-controlled origins are generated by Rif1 recruitment through Rap1 and Taz1 respectively 15,33 , implying that Rif1 can control the structure of late replication domains through pathways independent from the binding to telomeric factors. Among the known properties of Rif1, multimerization 34 , as well as binding to particular DNA conformations 35,36 or heterochromatin factors 20 {Dan, 2014 #4249} may play important roles in its chromatin domain-organizing role. The crosstalk between telomeres and heterochromatin has important implications, since the telomere changes that occur during development and aging can impact heterochromatin replication genome-wide.…”

The RGG domain in the C-terminus of the DEAD box helicases Dbp2 and Ded1 is necessary for G-quadruplex destabilization

“…The S. pombe Pfh1 and Rif1 proteins bind to G4 structures in vitro ( 47–49 ). Pfh1 is a 5′–3′ helicase from the Pif1 family that resolves G4 DNA structures and thus ensures genomic stability ( 36 , 47 , 50–51 ), while Rif1 is a telomere-associated protein that also has a role in regulating replication timing ( 49 , 52–53 ). In this study, we sought to identify new G4-binding proteins from S. pombe and thus to contribute to enhancing our knowledge about the G4 interactome and to provide insights into the relevance of G4s in different species.…”

Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex

“…10 Further, Rif1, a protein controlling the replication timing in yeast, specically interacts with its target G4, which adopts parallel topology. 11 Thus, ligands that selectively interact with or control each topology in G4 are expected to be useful tools for elucidating the biological functions of G4 structures.…”