Table 3 List of proteins affected by gene deletions highlighted in QFA screens
Standard NameComplexDescription from Saccharomyces Genome Database
Ddc19-1-1 sliding clampDNA damage checkpoint protein; part of a PCNA-like complex required for DDR, required for pachytene checkpoint to inhibit cell cycle in response to unrepaired recombination intermediates; potential Cdc28p substrate; forms nuclear foci upon DNA replication stress
Rad179-1-1 sliding clampCheckpoint protein; involved in the activation of the DNA damage and meiotic pachytene checkpoints; with Mec3p and Ddc1p, forms a clamp that is loaded onto partial duplex DNA; homolog of human and Schizosaccharomyces pombe Rad1 and Ustilago maydis Rec1 proteins
Rad249-1-1 sliding clampCheckpoint protein; involved in the activation of the DNA damage and meiotic pachytene checkpoints; subunit of a clamp loader that loads Rad17p-Mec3p-Ddc1p onto DNA; homolog of human and S. pombe Rad17 protein
Mre11MRX complexNuclease subunit of the MRX complex with Rad50p and Xrs2p; complex functions in repair of DNA DSBs and in telomere stability; Mre11p associates with Ser/Thr-rich ORFs in premeiotic phase; nuclease activity required for MRX function; widely conserved; forms nuclear foci upon DNA replication stress
Rad50MRX complexSubunit of MRX complex with Mre11p and Xrs2p; complex is involved in processing DNA DSBs in vegetative cells, initiation of meiotic DSBs, telomere maintenance, and nonhomologous end joining; forms nuclear foci upon DNA replication stress
Xrs2MRX complexProtein required for DNA repair; component of the Mre11 complex, which is involved in DSBs, meiotic recombination, telomere maintenance, and checkpoint signaling
Nam7NMDATP-dependent RNA helicase of the SFI superfamily; involved in NMD; required for efficient translation termination at nonsense codons and targeting of NMD substrates to P-bodies; binds to the small ribosomal subunit via an interaction with Rps26; forms cytoplasmic foci upon DNA replication stress
Nmd2NMDProtein involved in the NMD pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance
Upf3NMDComponent of the NMD pathway; along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
Yku70Ku heterodimerSubunit of the telomeric Ku complex (Yku70p-Yku80p); involved in telomere length maintenance, structure, and telomere position effect; required for localization of telomerase ribonucleoprotein to nucleus via interaction with the TLC1 guide RNA; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair
Yku80Ku heterodimerSubunit of the telomeric Ku complex (Yku70p-Yku80p); involved in telomere length maintenance, structure, and telomere position effect; required for localization of telomerase ribonucleoprotein via interaction with the TLC1 guide RNA; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair
Est1TelomeraseTLC1 RNA-associated factor involved in telomere length regulation; recruitment subunit of telomerase; has G-quadruplex promoting activity required for telomere elongation; possible role in activating telomere-bound Est2p-TLC1-RNA; EST1 has a paralog, EBS1, that arose from the whole genome duplication
Est2TelomeraseReverse transcriptase subunit of the telomerase holoenzyme; essential for telomerase core catalytic activity, involved in other aspects of telomerase assembly and function; mutations in human homolog are associated with aplastic anemia.
Est3TelomeraseComponent of the telomerase holoenzyme; involved in telomere replication
Rif1Rap1 interacting factorProtein that binds to the Rap1p C-terminus; acts synergistically with Rif2p to help control telomere length and establish telomeric silencing; involved in control of DNA replication; contributes to resection of DNA DSBs; deletion results in telomere elongation
Rif2Rap1 interacting factorProtein that binds to the Rap1p C-terminus; acts synergistically with Rif1p to help control telomere length and establish telomeric silencing; deletion results in telomere elongation; RIF2 has a paralog, ORC4, that arose from the whole genome duplication
Rad9DNA damage-dependent checkpoint protein; required for cell-cycle arrest in G1/S, intra-S, and G2/M, plays a role in postreplication repair (PRR) pathway; transmits checkpoint signal by activating Rad53p and Chk1p; hyperphosphorylated by Mec1p and Tel1p; multiple cyclin dependent kinase consensus sites, and the C-terminal BRCT domain contribute to DNA damage checkpoint activation; Rad9p Chk1 Activating Domain (CAD) is phosphorylated at multiple sites by Cdc28p/Clb2p
Chk1Serine/threonine kinase and DNA damage checkpoint effector; mediates cell cycle arrest via phosphorylation of Pds1p; phosphorylated by checkpoint signal transducer Mec1p; homolog of S. pombe and mammalian Chk1 checkpoint kinase
Tel1Protein kinase primarily involved in telomere length regulation; contributes to cell cycle checkpoint control in response to DNA damage; acts with Red1p and Mec1p to promote interhomolog recombination by phosphorylation of Hop1; functionally redundant with Mec1p; regulates P-body formation induced by replication stress; homolog of human ataxia-telangiectasia mutated (ATM) gene
Exo15′–3′ exonuclease and flap-endonuclease; involved in recombination, DSB repair, MMS2 error-free branch of the PRR pathway and DNA mismatch repair; role in telomere maintenance; member of the Rad2p nuclease family, with conserved N and I nuclease domains; relative distribution to the nucleus increases upon DNA replication stress; EXO1 has a paralog, DIN7, that arose from the whole genome duplication