@article{%a1.%Y_134,

title = {FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability},

author = {Boavida A and Napolitano LM and Santos D and Cortone G and Jegadesan NK and Onesti S and Branzei D and Pisani FM.},

url = {https://www.embopress.org/doi/full/10.1038/s44319-023-00044-y},

doi = {10.1038/s44319-023-00044-y},

year  = {2024},

date = {2024-02-07},

urldate = {2024-02-12},

journal = {EMBO reports},

volume = {25},

issue = {2},

pages = {876-901},

abstract = {FANCJ, a DNA helicase linked to Fanconi anemia and frequently mutated in cancers, counteracts replication stress by dismantling unconventional DNA secondary structures (such as G-quadruplexes) that occur at the DNA replication fork in certain sequence contexts. However, how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several other factors at DNA replication forks. The interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in cells unchallenged or treated with Pyridostatin, a G-quadruplex-binder, or Mitomycin C, a DNA inter-strand cross-linking agent. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding and enhanced DNA damage, a finding that suggests their potential role in cancer predisposition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_140,

title = {SnapShot: DNA repair pathways},

author = {Nunomiya A and Szakal B and Branzei D},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1097276523009759?via%3Dihub},

doi = {10.1016/j.molcel.2023.11.030},

year  = {2024},

date = {2024-02-12},

journal = {Molecular cell},

volume = {84},

issue = {1},

pages = {180},

abstract = {The genetic information stored in DNA is under continuous threat by endogenous and environmental sources of DNA damage. Cells have evolved multiple DNA repair pathways that function in overlapping manners, with principles shared across species. Here, we depict the main DNA repair pathways cells rely on, with the primary lesions they are tackling, along with key players and main DNA transactions. To view this SnapShot, open or download the PDF.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_145,

title = {SnapShot: Tolerating replication stress},

author = {Szakal B and Giannattasio M and Branzei D},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1097276523009760?via%3Dihub},

doi = {10.1016/j.molcel.2023.11.031},

year  = {2024},

date = {2024-02-13},

urldate = {2024-02-13},

journal = {Molecular cell},

volume = {84},

issue = {1},

pages = {182},

abstract = {Completion of DNA replication relies on the ability of replication forks to traverse various types of DNA damage, actively transcribed regions, and structured DNA. The mechanisms enabling these processes are here referred to as DNA damage tolerance pathways. Here, we depict the stalled DNA replication fork structures with main DNA transactions and key factors contributing to the bypass of such blocks, replication restart, and completion. To view this SnapShot, open or download the PDF.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_122,

title = {Hot on RAD51C: structure and functions of RAD51C-XRCC3},

author = {Szakal B and Branzei D},

url = {https://febs.onlinelibrary.wiley.com/doi/10.1002/1878-0261.13518},

doi = {10.1002/1878-0261.13518},

year  = {2023},

date = {2023-10-05},

urldate = {2023-10-05},

journal = {Molecular oncology},

volume = {17},

issue = {10},

pages = {1950-1952},

abstract = {A new study by Longo, Roy et al. has solved the structure of the RAD51C-XRCC3 (CX3) heterodimer with a bound ATP analog, identifying two main structural interfaces and defining separable replication fork stability roles. One function relates to the ability of RAD51C to bind and assemble CX3 on nascent DNA, with an impact on the ability of forks to restart upon replication stress. The other relates to effective CX3 heterodimer formation, required for 5' RAD51 filament capping, with effects on RAD51 filament disassembly, fork protection and influencing the persistence of reversed forks.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_121,

title = {PCNA recruits cohesin loader Scc2 to ensure sister chromatid cohesion},

author = {Psakhye I and Kawasumi R and Abe T and Hirota K and Branzei D},

url = {https://www.nature.com/articles/s41594-023-01064-x},

doi = {10.1038/s41594-023-01064-x.},

year  = {2023},

date = {2023-10-05},

journal = {Nature structural & molecular biology},

volume = {30},

issue = {9},

pages = {1286-1294},

abstract = {Sister chromatid cohesion, established during replication by the ring-shaped multiprotein complex cohesin, is essential for faithful chromosome segregation. Replisome-associated proteins are required to generate cohesion by two independent pathways. One mediates conversion of cohesins bound to unreplicated DNA ahead of replication forks into cohesive entities behind them, while the second promotes cohesin de novo loading onto newly replicated DNA. The latter process depends on the cohesin loader Scc2 (NIPBL in vertebrates) and the alternative PCNA loader CTF18-RFC. However, the mechanism of de novo cohesin loading during replication is unknown. Here we show that PCNA physically recruits the yeast cohesin loader Scc2 via its C-terminal PCNA-interacting protein motif. Binding to PCNA is crucial, as the scc2-pip mutant deficient in Scc2-PCNA interaction is defective in cohesion when combined with replisome mutants of the cohesin conversion pathway. Importantly, the role of NIPBL recruitment to PCNA for cohesion generation is conserved in vertebrate cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybi,

title = {Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4},

author = {Kannan A and Cuartas J and Gangwani P and Branzei D and Gangwani L},

url = {https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awab464/6511590},

doi = {10.1093/brain/awab464},

year  = {2022},

date = {2022-03-21},

journal = {Brain},

abstract = {Mutation in the Senataxin (SETX) gene causes an autosomal dominant neuromuscular disorder, amyotrophic lateral sclerosis 4 (ALS4), characterized by degeneration of motor neurons, muscle weakness and atrophy. SETX is an RNA-DNA helicase that mediates resolution of co-transcriptional RNA-DNA hybrids (R-loops). The process of R-loop resolution is essential for the normal functioning of cells, including neurons. The molecular basis of ALS4 pathogenesis and the mechanism of R-loop resolution are unclear. We report that the zinc finger protein ZPR1 binds to RNA-DNA hybrids, recruits SETX onto R-loops and is critical for R-loop resolution. ZPR1 deficiency disrupts the integrity of R-loop resolution complexes (RLRC) containing SETX and causes increased R-loop accumulation throughout gene transcription. We uncover that SETX is a downstream target of ZPR1 and that overexpression of ZPR1 can rescue RLRC assembly in SETX-deficient cells but not vice versa. To uncover the mechanism of R-loop resolution, we examined the function of SETX-ZPR1 complexes using two genetic motor neuron disease models with altered R-loop resolution. Notably, chronic low levels of SETX-ZPR1 complexes onto R-loops result in a decrease of R-loop resolution activity causing an increase in R-loop levels in spinal muscular atrophy (SMA). ZPR1 overexpression increases recruitment of SETX onto R-loops, decreases R-loops and rescues the SMA phenotype in motor neurons and patient cells. Strikingly, interaction of SETX with ZPR1 is disrupted in ALS4 patients that have heterozygous SETX (L389S) mutation. ZPR1 fails to recruit the mutant SETX homodimer but recruits the heterodimer with partially disrupted interaction between SETX and ZPR1. Interestingly, disruption of SETX-ZPR1 complexes causes increase in R-loop resolution activity leading to fewer R-loops in ALS4. Modulation of ZPR1 levels regulates R-loop accumulation and rescues the pathogenic R-loop phenotype in ALS4 patient cells. These findings originate a new concept, "opposite alterations in a cell biological activity (R-loop resolution) result in similar pathogenesis (neurodegeneration) in different genetic motor neuron disorders". We propose that ZPR1 collaborates with SETX and may function as a molecular brake to regulate SETX-dependent R-loop resolution activity critical for the normal functioning of motor neurons.},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{%a1.%Ybg,

title = {Parental histone deposition on the replicated strands promotes error-free DNA damage tolerance and regulates drug resistance},

author = {Dolce V and Dusi S and Giannattasio M and Joseph CR and Fumasoni M and Branzei D},

url = {http://genesdev.cshlp.org/content/early/2022/02/01/gad.349207.121.long},

doi = {10.1101/gad.349207.121},

year  = {2022},

date = {2022-03-21},

urldate = {2022-03-21},

journal = {Genes & development},

volume = {36},

issue = {1-4},

pages = {167-179},

abstract = {Ctf4 is a conserved replisome component with multiple roles in DNA metabolism. To investigate connections between Ctf4-mediated processes involved in drug resistance, we conducted a suppressor screen of ctf4delta sensitivity to the methylating agent MMS. We uncovered that mutations in Dpb3 and Dpb4 components of polymerase ε result in the development of drug resistance in ctf4Δ via their histone-binding function. Alleviated sensitivity to MMS of the double mutants was not associated with rescue of ctf4delta defects in sister chromatid cohesion, replication fork architecture, or template switching, which ensures error-free replication in the presence of genotoxic stress. Strikingly, the improved viability depended on translesion synthesis (TLS) polymerase-mediated mutagenesis, which was drastically increased in ctf4 dpb3 double mutants. Importantly, mutations in Mcm2-Ctf4-Polα and Dpb3-Dpb4 axes of parental (H3-H4)2 deposition on lagging and leading strands invariably resulted in reduced error-free DNA damage tolerance through gap filling by template switch recombination. Overall, we uncovered a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_29,

title = {Rad51-mediated replication of damaged templates relies on monoSUMOylated DDK kinase},

author = {Joseph CR and Dusi S and Giannattasio M and Branzei D},

url = {https://www.nature.com/articles/s41467-022-30215-9},

doi = {10.1038/s41467-022-30215-9},

year  = {2022},

date = {2022-08-25},

journal = {Nature communications},

volume = {13},

issue = {1},

pages = {2480},

abstract = {DNA damage tolerance (DDT), activated by replication stress during genome replication, is mediated by translesion synthesis and homologous recombination (HR). Here we uncover that DDK kinase, essential for replication initiation, is critical for replication-associated recombination-mediated DDT. DDK relies on its multi-monoSUMOylation to facilitate HR-mediated DDT and optimal retention of Rad51 recombinase at replication damage sites. Impairment of DDK kinase activity, reduced monoSUMOylation and mutations in the putative SUMO Interacting Motifs (SIMs) of Rad51 impair replication-associated recombination and cause fork uncoupling with accumulation of large single-stranded DNA regions at fork branching points. Notably, genetic activation of salvage recombination rescues the uncoupled fork phenotype but not the recombination-dependent gap-filling defect of DDK mutants, revealing that the salvage recombination pathway operates preferentially proximal to fork junctions at stalled replication forks. Overall, we uncover that monoSUMOylated DDK acts with Rad51 in an axis that prevents replication fork uncoupling and mediates recombination-dependent gap-filling.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_65,

title = {Computed structures of core eukaryotic protein complexes.},

author = {Humphreys IR and Pei J and Baek M and Krishnakumar A and Anishchenko I and Ovchinnikov S and Zhang J and Ness TJ and Banjade S and Bagde SR and Stancheva VG and Li XH and Liu K and Zheng Z and Barrero DJ and Roy U and Kuper J and Fernández IS and Szakal B and Branzei D and Rizo J and Kisker C and Greene EC and Biggins S and Keeney S and Miller EA and Fromme JC and Hendrickson TL and Cong Q and Baker D},

url = {https://www.science.org/doi/10.1126/science.abm4805?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},

doi = {10.1126/science.abm4805},

year  = {2021},

date = {2021-12-14},

journal = {Science},

volume = {374},

number = {6573},

abstract = {Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coevolution analysis and deep-learning–based structure modeling to systematically identify and build accurate models of core eukaryotic protein complexes within the Saccharomyces cerevisiae proteome. We use a combination of RoseTTAFold and AlphaFold to screen through paired multiple sequence alignments for 8.3 million pairs of yeast proteins, identify 1505 likely to interact, and build structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects.},

author = {Jegadesan NK and Branzei D},

url = {https://www.pnas.org/content/118/17/e2024258118.long},

doi = {10.1073/pnas.2024258118},

year  = {2021},

date = {2021-05-17},

urldate = {2021-05-17},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {118},

number = {17},

pages = {e2024258118},

abstract = {DDX11 encodes an iron-sulfur cluster DNA helicase required for development, mutated, and overexpressed in cancers. Here, we show that loss of DDX11 causes replication stress and sensitizes cancer cells to DNA damaging agents, including poly ADP ribose polymerase (PARP) inhibitors and platinum drugs. We find that DDX11 helicase activity prevents chemotherapy drug hypersensitivity and accumulation of DNA damage. Mechanistically, DDX11 acts downstream of 53BP1 to mediate homology-directed repair and RAD51 focus formation in manners nonredundant with BRCA1 and BRCA2. As a result, DDX11 down-regulation aggravates the chemotherapeutic sensitivity of BRCA1/2-mutated cancers and resensitizes chemotherapy drug-resistant BRCA1/2-mutated cancer cells that regained homologous recombination proficiency. The results further indicate that DDX11 facilitates recombination repair by assisting double strand break resection and the loading of both RPA and RAD51 on single-stranded DNA substrates. We propose DDX11 as a potential target in cancers by creating pharmacologically exploitable DNA repair vulnerabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybu,

title = {DNA helicases in homologous recombination repair},

author = {Branzei D and Szakal B},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0959437X21000794?via%3Dihub},

doi = {10.1016/j.gde.2021.06.009},

year  = {2021},

date = {2021-08-25},

urldate = {2021-08-25},

journal = {Current opinion in genetics & development},

volume = {71},

pages = {27-33},

abstract = {Helicases are in the spotlight of DNA metabolism and are critical for DNA repair in all domains of life. At their biochemical core, they bind and hydrolyze ATP, converting this energy to translocate unidirectionally, with different strand polarities and substrate binding specificities, along one strand of a nucleic acid. In doing so, DNA and RNA helicases separate duplex strands or remove nucleoprotein complexes, affecting DNA repair and the architecture of replication forks. In this review, we focus on recent advances on the roles and regulations of DNA helicases in homologous recombination repair, a critical pathway for mending damaged chromosomes and for ensuring genome integrity. Copyright 2021 Elsevier Ltd. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybv,

title = {SMC complexes are guarded by the SUMO protease Ulp2 against SUMO-chain-mediated turnover},

author = {Psakhye I and Branzei D},

url = {https://www.sciencedirect.com/science/article/pii/S2211124721009128?via%3Dihub},

doi = {10.1016/j.celrep.2021.109485},

year  = {2021},

date = {2021-08-25},

journal = {Cell reports},

volume = {36},

number = {5},

abstract = {Structural maintenance of chromosomes (SMCs) complexes, cohesin, condensin, and Smc5/6, are essential for viability and participate in multiple processes, including sister chromatid cohesion, chromosome condensation, and DNA repair. Here we show that SUMO chains target all three SMC complexes and are antagonized by the SUMO protease Ulp2 to prevent their turnover. We uncover that the essential role of the cohesin-associated subunit Pds5 is to counteract SUMO chains jointly with Ulp2. Importantly, fusion of Ulp2 to kleisin Scc1 supports viability of PDS5 null cells and protects cohesin from proteasomal degradation mediated by the SUMO-targeted ubiquitin ligase Slx5/Slx8. The lethality of PDS5-deleted cells can also be bypassed by simultaneous loss of the proliferating cell nuclear antigen (PCNA) unloader, Elg1, and the cohesin releaser, Wpl1, but only when Ulp2 is functional. Condensin and Smc5/6 complex are similarly guarded by Ulp2 against unscheduled SUMO chain assembly, which we propose to time the availability of SMC complexes on chromatin.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y__511,

title = {Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites.},

author = {Agashe S and Joseph CR and Reyes TAC and Menolfi D and Giannattasio M and Waizenegger A and Szakal B and Branzei D},

url = {https://www.nature.com/articles/s41467-021-22217-w},

doi = {10.1038/s41467-021-22217-w},

year  = {2021},

date = {2021-04-14},

urldate = {2021-04-14},

journal = {Nature communications},

volume = {12},

number = {1},

pages = {2111},

abstract = {Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. We isolate an intra-allelic suppressor of smc6-56 proficient in Top3 retention but affected in pathways that act complementarily with Sgs1 and Top3 to resolve JMs arising at replication termination. Upon replication stress, the smc6-56 suppressor requires STR and Mus81-Mms4 functions for recovery, but not Srs2 and Mph1 helicases that prevent maturation of recombination intermediates. Thus, Smc5/6 functions jointly with Top3 and STR to mediate replication completion and influences the function of other DNA crossed-strand processing enzymes at NPSs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Ybvw,

title = {Vertebrate CTF18 and DDX11 essential function in cohesion is bypassed by preventing WAPL-mediated cohesin release},

author = {Kawasumi R and Abe T and Psakhye I and Miyata K and Hirota K and Branzei D},

url = {http://genesdev.cshlp.org/content/35/19-20/1368.long},

doi = {10.1101/gad.348581.121},

year  = {2021},

date = {2021-11-08},

urldate = {2021-11-08},

journal = {Genes & development},

volume = {35},

number = {19-20},

pages = {1368-1382},

abstract = {The alternative PCNA loader containing CTF18-DCC1-CTF8 facilitates sister chromatid cohesion (SCC) by poorly defined mechanisms. Here we found that in DT40 cells, CTF18 acts complementarily with the Warsaw breakage syndrome DDX11 helicase in mediating SCC and proliferation. We uncover that the lethality and cohesion defects of ctf18 ddx11 mutants are associated with reduced levels of chromatin-bound cohesin and rescued by depletion of WAPL, a cohesin-removal factor. On the contrary, high levels of ESCO1/2 acetyltransferases that acetylate cohesin to establish SCC do not rescue ctf18 ddx11 phenotypes. Notably, the tight proximity of sister centromeres and increased anaphase bridges characteristic of WAPL-depleted cells are abrogated by loss of both CTF18 and DDX11 The results reveal that vertebrate CTF18 and DDX11 collaborate to provide sufficient amounts of chromatin-loaded cohesin available for SCC generation in the presence of WAPL-mediated cohesin-unloading activity. This process modulates chromosome structure and is essential for cellular proliferation in vertebrates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_483,

title = {Mus81-Mms4 endonuclease is an Esc2-STUbL-Cullin8 mitotic substrate impacting on genome integrity. },

author = {Waizenegger A and Urulangodi M and Lehmann CP and Reyes TAC and Saugar I and Tercero JA and Szakal B and Branzei D},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7665200/},

doi = {10.1038/s41467-020-19503-4},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Nature communications},

volume = {11},

number = {1},

pages = {5746},

abstract = {The Mus81-Mms4 nuclease is activated in G2/M via Mms4 phosphorylation to allow resolution of persistent recombination structures. However, the fate of the activated phosphorylated Mms4 remains unknown. Here we find that Mms4 is engaged by (poly)SUMOylation and ubiquitylation and targeted for proteasome degradation, a process linked to the previously described Mms4 phosphorylation cycle. Mms4 is a mitotic substrate for the SUMO-Targeted Ubiquitin ligase Slx5/8, the SUMO-like domain-containing protein Esc2, and the Mms1-Cul8 ubiquitin ligase. In the absence of these activities, phosphorylated Mms4 accumulates on chromatin in an active state in the next G1, subsequently causing abnormal processing of replication-associated recombination intermediates and delaying the activation of the DNA damage checkpoint. Mus81-Mms4 mutants that stabilize phosphorylated Mms4 have similar detrimental effects on genome integrity. Overall, our findings highlight a replication protection function for Esc2-STUbL-Cul8 and emphasize the importance for genome stability of resetting phosphorylated Mms4 from one cycle to another.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_455,

title = {Prevention of unwanted recombination at damaged replication forks},

author = {Lehmann CP and Jimenez-Martín A and Branzei D and Tercero JA},

url = {https://link.springer.com/article/10.1007/s00294-020-01095-7},

doi = {10.1007/s00294-020-01095-7},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Current genetics},

volume = {66},

number = {6},

pages = {1045-1051},

abstract = {Homologous recombination is essential for the maintenance of genome integrity but must be strictly controlled to avoid dangerous outcomes that produce the opposite effect, genomic instability. During unperturbed chromosome replication, recombination is globally inhibited at ongoing DNA replication forks, which helps to prevent deleterious genomic rearrangements. This inhibition is carried out by Srs2, a helicase that binds to SUMOylated PCNA and has an anti-recombinogenic function at replication forks. However, at damaged stalled forks, Srs2 is counteracted and DNA lesion bypass can be achieved by recombination-mediated template switching. In budding yeast, template switching is dependent on Rad5. In the absence of this protein, replication forks stall in the presence of DNA lesions and cells die. Recently, we showed that in cells lacking Rad5 that are exposed to DNA damage or replicative stress, elimination of the conserved Mgs1/WRNIP1 ATPase allows an alternative mode of DNA damage bypass that is driven by recombination and facilitates completion of chromosome replication and cell viability. We have proposed that Mgs1 is important to prevent a potentially harmful salvage pathway of recombination at damaged stalled forks. In this review, we summarize our current understanding of how unwanted recombination is prevented at damaged stalled replication forks.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_98,

title = {SMC5/6 acts jointly with Fanconi anemia factors to support DNA repair and genome stability.},

author = {Rossi F and Helbling-Leclerc A and Kawasumi R and Jegadesan NK and Xu X and Devulder P and Abe T and Takata M and Xu D and Rosselli F and Branzei D},

url = {https://www.embopress.org/doi/full/10.15252/embr.201948222},

doi = {10.15252/embr.201948222},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {EMBO reports},

volume = {21},

number = {2},

pages = {e48222},

abstract = {SMC5/6 function in genome integrity remains elusive. Here, we show that SMC5 dysfunction in avian DT40 B cells causes mitotic delay and hypersensitivity toward DNA intra- and inter-strand crosslinkers (ICLs), with smc5 mutants being epistatic to FANCC and FANCM mutations affecting the Fanconi anemia (FA) pathway. Mutations in the checkpoint clamp loader RAD17 and the DNA helicase DDX11, acting in an FA-like pathway, do not aggravate the damage sensitivity caused by SMC5 dysfunction in DT40 cells. SMC5/6 knockdown in HeLa cells causes MMC sensitivity, increases nuclear bridges, micronuclei, and mitotic catastrophes in a manner similar and non-additive to FANCD2 knockdown. In both DT40 and HeLa systems, SMC5/6 deficiency does not affect FANCD2 ubiquitylation and, unlike FANCD2 depletion, RAD51 focus formation. SMC5/6 components further physically interact with FANCD2-I in human cells. Altogether, our data suggest that SMC5/6 functions jointly with the FA pathway to support genome integrity and DNA repair and may be implicated in FA or FA-related human disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_454,

title = {The Mgs1/WRNIP1 ATPase Is Required to Prevent a Recombination Salvage Pathway at Damaged Replication Forks},

author = {{Jimenez-Martin A} and Saugar I and Joseph CR and Mayer A and Lehmann CP and Szakal B and Branzei D and Tercero JA},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141828/},

doi = {10.1126/sciadv.aaz3327},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Science advances},

volume = {6},

number = {15},

abstract = {DNA damage tolerance (DDT) is crucial for genome integrity maintenance. DDT is mainly carried out by template switch recombination, an error-free mode of overcoming DNA lesions, or translesion DNA synthesis, which is error-prone. Here, we investigated the role of Mgs1/WRNIP1 in modulating DDT. Using budding yeast, we found that elimination of Mgs1 in cells lacking Rad5, an essential protein for DDT, activates an alternative mode of DNA damage bypass, driven by recombination, which allows chromosome replication and cell viability under stress conditions that block DNA replication forks. This salvage pathway is RAD52 and RAD59 dependent, requires the DNA polymerase δ and PCNA modification at K164, and is enabled by Esc2 and the PCNA unloader Elg1, being inhibited when Mgs1 is present. We propose that Mgs1 is necessary to prevent a potentially toxic recombination salvage pathway at sites of perturbed replication, which, in turn, favors Rad5-dependent template switching, thus helping to preserve genome stability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y%_37,

title = {DNA Replication Through Strand Displacement During Lagging Strand DNA Synthesis in Saccharomyces cerevisiae.},

author = {Giannattasio M and Branzei D},

url = {https://www.mdpi.com/2073-4425/10/2/167},

doi = {10.3390/genes10020167},

year  = {2019},

date = {2019-08-15},

journal = {Genes (Basel)},

volume = {10},

number = {2},

pages = {E167},

abstract = {This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the eukaryotic replisome, we discuss studies on bacterial, bacteriophage and viral DNA polymerases with potent strand displacement activities. We describe proposed pathways of Okazaki fragment processing via short and long flaps, with a focus on experimental results obtained in Saccharomyces cerevisiae that suggest the existence of frequent and extended strand displacement events during eukaryotic lagging strand DNA synthesis, and comment on their implications for genome integrity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y%_35,

title = {Rad5 Recruits Error-Prone DNA Polymerases for Mutagenic Repair of ssDNA Gaps on Undamaged Templates.},

author = {Gallo D and Kim T and Szakal B and Saayman X and Narula A and Park Y and Branzei D and Zhang Z and Brown GW},

url = {https://www.sciencedirect.com/science/article/abs/pii/S1097276519300012?via%3Dihub},

doi = {10.1016/j.molcel.2019.01.001},

year  = {2019},

date = {2019-08-15},

journal = {Molecular cell},

volume = {73},

number = {5},

pages = {900-914},

abstract = {Post-replication repair (PRR) allows tolerance of chemical- and UV-induced DNA base lesions in both an error-free and an error-prone manner. In classical PRR, PCNA monoubiquitination recruits translesion synthesis (TLS) DNA polymerases that can replicate through lesions. We find that PRR responds to DNA replication stress that does not cause base lesions. Rad5 forms nuclear foci during normal S phase and after exposure to types of replication stress where DNA base lesions are likely absent. Rad5 binds to the sites of stressed DNA replication forks, where it recruits TLS polymerases to repair single-stranded DNA (ssDNA) gaps, preventing mitotic defects and chromosome breaks. In contrast to the prevailing view of PRR, our data indicate that Rad5 promotes both mutagenic and error-free repair of undamaged ssDNA that arises during physiological and exogenous replication stress. Copyright 2019 Elsevier Inc. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_75,

title = {SUMO-Chain-Regulated Proteasomal Degradation Timing Exemplified in DNA Replication Initiation.},

author = {Psakhye I and Castellucci F and Branzei D},

url = {https://www.sciencedirect.com/science/article/pii/S1097276519306197?via%3Dihub},

doi = {10.1016/j.molcel.2019.08.003.},

year  = {2019},

date = {2019-08-15},

journal = {Molecular cell},

volume = {76},

number = {4},

pages = {632-645},

abstract = {Similar to ubiquitin, SUMO forms chains, but the identity of SUMO-chain-modified factors and the purpose of this modification remain largely unknown. Here, we identify the budding yeast SUMO protease Ulp2, able to disassemble SUMO chains, as a DDK interactor enriched at replication origins that promotes DNA replication initiation. Replication-engaged DDK is SUMOylated on chromatin, becoming a degradation-prone substrate when Ulp2 no longer protects it against SUMO chain assembly. Specifically, SUMO chains channel DDK for SUMO-targeted ubiquitin ligase Slx5/Slx8-mediated and Cdc48 segregase-assisted proteasomal degradation. Importantly, the SUMOylation-defective ddk-KR mutant rescues inefficient replication onset and MCM activation in cells lacking Ulp2, suggesting that SUMO chains time DDK degradation. Using two unbiased proteomic approaches, we further identify subunits of the MCM helicase and other factors as SUMO-chain-modified degradation-prone substrates of Ulp2 and Slx5/Slx8. We thus propose SUMO-chain/Ulp2-protease-regulated proteasomal degradation as a mechanism that times the availability of functionally engaged SUMO-modified protein pools during replication and beyond.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_105,

title = {AND-1 fork protection function prevents fork resection and is essential for proliferation.},

author = {Abe T and Kawasumi R and Giannattasio M and Dusi S and Yoshimoto Y and Miyata K and Umemura K and Hirota K and Branzei D},

url = {https://www.nature.com/articles/s41467-018-05586-7},

doi = {10.1038/s41467-018-05586-7},

year  = {2018},

date = {2018-08-16},

journal = {Nature Communications},

volume = {9},

number = {1},

pages = {3091},

abstract = {AND-1/Ctf4 bridges the CMG helicase and DNA polymerase alpha, facilitating replication. Using an inducible degron system in avian cells, we find that AND-1 depletion is incompatible with proliferation, owing to cells accumulating in G2 with activated DNA damage checkpoint. Replication without AND-1 causes fork speed slow-down and accumulation of long single-stranded DNA (ssDNA) gaps at the replication fork junction, with these regions being converted to DNA double strand breaks (DSBs) in G2. Strikingly, resected forks and DNA damage accumulation in G2, but not fork slow-down, are reverted by treatment with mirin, an MRE11 nuclease inhibitor. Domain analysis of AND-1 further revealed that the HMG box is important for fast replication but not for proliferation, whereas conversely, the WD40 domain prevents fork resection and subsequent DSB-associated lethality. Thus, our findings uncover a fork protection function of AND-1/Ctf4 manifested via the WD40 domain that is essential for proliferation and averts genome instability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_148,

title = {Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy.},

author = {Kannan A and Bhatia K and Branzei D and Gangwani L},

url = {https://academic.oup.com/nar/article/46/16/8326/5054094},

doi = {10.1093/nar/gky641},

year  = {2018},

date = {2018-08-16},

journal = {Nucleic Acids Research},

volume = {46},

number = {16},

pages = {8326-8346},

abstract = {Chronic low levels of survival motor neuron (SMN) protein cause spinal muscular atrophy (SMA). SMN is ubiquitously expressed, but the mechanisms underlying predominant neuron degeneration in SMA are poorly understood. We report that chronic low levels of SMN cause Senataxin (SETX)-deficiency, which results in increased RNA–DNA hybrids (R-loops) and DNA double-strand breaks (DSBs), and deficiency of DNA-activated protein kinase-catalytic subunit (DNA-PKcs), which impairs DSB repair. Consequently, DNA damage accumulates in patient cells, SMA mice neurons and patient spinal cord tissues. In dividing cells, DSBs are repaired by homologous recombination (HR) and non-homologous end joining (NHEJ) pathways, but neurons predominantly use NHEJ, which relies on DNA-PKcs activity. In SMA dividing cells, HR repairs DSBs and supports cellular proliferation. In SMA neurons, DNA-PKcs-deficiency causes defects in NHEJ-mediated repair leading to DNA damage accumulation and neurodegeneration. Restoration of SMN levels rescues SETX and DNA-PKcs deficiencies and DSB accumulation in SMA neurons and patient cells. Moreover, SETX overexpression in SMA neurons reduces R-loops and DNA damage, and rescues neurodegeneration. Our findings identify combined deficiency of SETX and DNA-PKcs stemming downstream of SMN as an underlying cause of DSBs accumulation, genomic instability and neurodegeneration in SMA and suggest SETX as a potential therapeutic target for SMA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_104,

title = {Damage Tolerance Mechanisms Revealed from the Analysis of Immunoglobulin V Gene Diversification in Avian DT40 Cells.},

author = {Abe T and Branzei D and Hirota K},

url = {https://www.mdpi.com/2073-4425/9/12/614},

doi = {10.3390/genes9120614},

year  = {2018},

date = {2018-08-16},

journal = {Genes},

volume = {9},

number = {12},

pages = {614},

abstract = {DNA replication is an essential biochemical reaction in dividing cells that frequently stalls at damaged sites. Homologous/homeologous recombination (HR)-mediated template switch and translesion DNA synthesis (TLS)-mediated bypass processes release arrested DNA replication forks. These mechanisms are pivotal for replication fork maintenance and play critical roles in DNA damage tolerance (DDT) and gap-filling. The avian DT40 B lymphocyte cell line provides an opportunity to examine HR-mediated template switch and TLS triggered by abasic sites by sequencing the constitutively diversifying immunoglobulin light-chain variable gene (IgV). During IgV diversification, activation-induced deaminase (AID) converts dC to dU, which in turn is excised by uracil DNA glycosylase and yields abasic sites within a defined window of around 500 base pairs. These abasic sites can induce gene conversion with a set of homeologous upstream pseudogenes via the HR-mediated template switch, resulting in templated mutagenesis, or can be bypassed directly by TLS, resulting in non-templated somatic hypermutation at dC/dG base pairs. In this review, we discuss recent works unveiling IgV diversification mechanisms in avian DT40 cells, which shed light on DDT mode usage in vertebrate cells and tolerance of a basic sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_153,

title = {Error-free DNA damage tolerance pathway is facilitated by the Irc5 translocase through cohesin.},

author = {Litwin I and Bakowski T and Szakal B and Pilarczyk E and Maciaszczyk-Dziubinska E and Branzei D and Wysocki R},

url = {http://emboj.embopress.org/content/37/18/e98732.long},

doi = {10.15252/embj.201798732},

year  = {2018},

date = {2018-08-15},

journal = {Embo Journal},

volume = {37},

number = {18},

pages = {e98732},

abstract = {DNA damage tolerance (DDT) mechanisms facilitate replication resumption and completion when DNA replication is blocked by bulky DNA lesions. In budding yeast, template switching (TS) via the Rad18/Rad5 pathway is a favored DDT pathway that involves usage of the sister chromatid as a template to bypass DNA lesions in an error-free recombination-like process. Here, we establish that the Snf2 family translocase Irc5 is a novel factor that promotes TS and averts single-stranded DNA persistence during replication. We demonstrate that, during replication stress, Irc5 enables replication progression by assisting enrichment of cohesin complexes, recruited in an Scc2/Scc4-dependent fashion, near blocked replication forks. This allows efficient formation of sister chromatid junctions that are crucial for error-free DNA lesion bypass. Our results support the notion of a key role of cohesin in the completion of DNA synthesis under replication stress and reveal that the Rad18/Rad5-mediated DDT pathway is linked to cohesin enrichment at sites of perturbed replication via the Snf2 family translocase Irc5.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_146,

title = {Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae.},

author = {Iacovella MG and Bremang M and Basha O and Giacò L and Carotenuto W and Golfieri C and Szakal B and Dal Maschio M and Infantino V and Beznoussenko GV and Joseph CR and Visintin C and Mironov AA and Visintin R and Branzei D and Ferreira-Cerca S and Yeger-Lotem E and De Wulf P},

url = {https://academic.oup.com/nar/article/46/15/7586/5054092},

doi = {10.1093/nar/gky618},

year  = {2018},

date = {2018-08-16},

journal = {Nucleic Acids Research},

volume = {46},

number = {15},

pages = {7586-7611},

abstract = {The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_120,

title = {SIRFing the replication fork: Assessing protein interactions with nascent DNA},

author = {Branzei D and Giannattasio M},

url = {http://jcb.rupress.org/content/217/4/1177.long},

doi = {10.1083/jcb.201802083},

year  = {2018},

date = {2018-08-17},

journal = {Journal of Cell Biology},

volume = {217},

number = {4},

pages = {1177},

abstract = {Roy et al. (2018. J. Cell. Biol. https://doi.org/10.1083/jcb.201709121) describe an ingenious single-cell assay system, in situ analysis of protein interactions at DNA replication forks (SIRF), for the quantitative analysis of protein interactions with nascent DNA at active and stalled replication forks. The sensitive and accurate SIRF methodology is suitable for multiparameter measurements in cell populations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_163,

title = {SPARTAN promotes genetic diversification of the immunoglobulin-variable gene locus in avian DT40 cells.},

author = {Nakazato A and Kajita K and Ooka M and Akagawa R and Abe T and Takeda S and Branzei D and Hirota K},

url = {https://www.sciencedirect.com/science/article/pii/S1568786418300569?via%3Dihub},

doi = {10.1016/j.dnarep.2018.06.003},

year  = {2018},

date = {2018-08-16},

journal = {DNA Repair},

volume = {68},

pages = {50-57},

abstract = {Prolonged replication arrest on damaged templates is a cause of fork collapse, potentially resulting in genome instability. Arrested replication is rescued by translesion DNA synthesis (TLS) and homologous recombination (HR)-mediated template switching. SPARTAN, a ubiquitin-PCNA-interacting regulator, regulates TLS via mechanisms incompletely understood. Here we show that SPARTAN promotes diversification of the chicken DT40 immunoglobulin-variable λ gene by facilitating TLS-mediated hypermutation and template switch-mediated gene-conversion, both induced by replication blocks at abasic sites. SPARTAN-/- and SPARTAN-/-/Polη-/-/Polζ-/- cells showed defective and similar decrease in hypermutation rates, as well as alterations in the mutation spectra, with decreased dG-to-dC transversions and increased dG-to-dA transitions. Strikingly, SPARTAN-/- cells also showed reduced template switch-mediated gene-conversion at the immunoglobulin locus, while being proficient in HR-mediated double strand break repair, and sister chromatid recombination. Notably, SPARTAN's ubiquitin-binding zinc-finger 4 domain, but not the PCNA interacting peptide domain or its DNA-binding domain, was specifically required for the promotion of immunoglobulin gene-conversion, while all these three domains were shown to contribute similarly to TLS. In all, our results suggest that SPARTAN mediates TLS in concert with the Polη-Polζ pathway and that it facilitates HR-mediated template switching at a subset of stalled replication forks, potentially by interacting with unknown ubiquitinated proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_177,

title = {The Swr1 chromatin-remodeling complex prevents genome instability induced by replication fork progression defects.},

author = {Srivatsan A and Li BZ and Szakal B and Branzei D and Putnam CD and Kolodner RD},

url = {https://www.nature.com/articles/s41467-018-06131-2},

doi = {10.1038/s41467-018-06131-2},

year  = {2018},

date = {2018-08-10},

journal = {Nature Communications},

volume = {9},

number = {1},

pages = {3680},

abstract = {Genome instability is associated with tumorigenesis. Here, we identify a role for the histone Htz1, which is deposited by the Swr1 chromatin-remodeling complex (SWR-C), in preventing genome instability in the absence of the replication fork/replication checkpoint proteins Mrc1, Csm3, or Tof1. When combined with deletion of SWR1 or HTZ1, deletion of MRC1, CSM3, or TOF1 or a replication-defective mrc1 mutation causes synergistic increases in gross chromosomal rearrangement (GCR) rates, accumulation of a broad spectrum of GCRs, and hypersensitivity to replication stress. The double mutants have severe replication defects and accumulate aberrant replication intermediates. None of the individual mutations cause large increases in GCR rates; however, defects in MRC1, CSM3 or TOF1 cause activation of the DNA damage checkpoint and replication defects. We propose a model in which Htz1 deposition and retention in chromatin prevents transiently stalled replication forks that occur in mrc1, tof1, or csm3 mutants from being converted to DNA double-strand breaks that trigger genome instability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_106,

title = {Warsaw breakage syndrome DDX11 helicase acts jointly with RAD17 in the repair of bulky lesions and replication through abasic sites.},

author = {Abe T and Ooka M and Kawasumi R and Miyata K and Takata M and Hirota K and Branzei D},

url = {http://www.pnas.org/content/115/33/8412.long},

doi = {10.1073/pnas.1803110115},

year  = {2018},

date = {2018-08-16},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {115},

number = {33},

pages = {8412-8417},

abstract = {Warsaw breakage syndrome, a developmental disorder caused by mutations in the DDX11/ChlR1 helicase, shows cellular features of genome instability similar to Fanconi anemia (FA). Here we report that DDX11-deficient avian DT40 cells exhibit interstrand crosslink (ICL)-induced chromatid breakage, with DDX11 functioning as backup for the FA pathway in regard to ICL repair. Importantly, we establish that DDX11 acts jointly with the 9-1-1 checkpoint clamp and its loader, RAD17, primarily in a postreplicative fashion, to promote homologous recombination repair of bulky lesions, but is not required for intra-S checkpoint activation or efficient fork progression. Notably, we find that DDX11 also promotes diversification of the chicken Ig-variable gene, a process triggered by programmed abasic sites, by facilitating both hypermutation and homeologous recombination-mediated gene conversion. Altogether, our results uncover that DDX11 orchestrates jointly with 9-1-1 and its loader, RAD17, DNA damage tolerance at sites of bulky lesions, and endogenous abasic sites. These functions may explain the essential roles of DDX11 and its similarity with 9-1-1 during development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_192,

title = {ESCO1/2's roles in chromosome structure and interphase chromatin organization.},

author = {Kawasumi R and Abe T and Arakawa H and Garre M and Hirota K and Branzei D},

url = {http://genesdev.cshlp.org/content/31/21/2136.long},

doi = {10.1101/gad.306084.117},

year  = {2017},

date = {2017-08-10},

journal = {Genes and development},

volume = {31},

number = {21},

pages = {2136-2150},

abstract = {ESCO1/2 acetyltransferases mediating SMC3 acetylation and sister chromatid cohesion (SCC) are differentially required for genome integrity and development. Here we established chicken DT40 cell lines with mutations in ESCO1/2, SMC3 acetylation, and the cohesin remover WAPL. Both ESCO1 and ESCO2 promoted SCC, while ESCO2 was additionally and specifically required for proliferation and centromere integrity. ESCO1 overexpression fully suppressed the slow proliferation and centromeric separation phenotypes of esco2 cells but only partly suppressed its chromosome arm SCC defects. Concomitant inactivation of ESCO1 and ESCO2 caused lethality owing to compromised mitotic chromosome segregation. Neither wapl nor acetyl-mimicking smc3-QQ mutations rescued esco1 esco2 lethality. Notably, esco1 esco2 wapl conditional mutants showed very severe proliferation defects associated with catastrophic mitoses and also abnormal interphase chromatin organization patterns. The results indicate that cohesion establishment by vertebrate ESCO1/2 is linked to interphase chromatin architecture formation, a newly identified function of cohesin acetyltransferases that is both fundamentally and medically relevant.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}