Cited by 49DNA Repair MechanismsMicrotubule and mitosis dynamicsFungal and yeast genetics research

Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity

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Kottemann, Molly C., Conti, Brooke A., Lach, Francis P., Smogorzewska, Agata·2018·Molecular Cell

Abstract

The protection and efficient restart of stalled replication forks is critical for the maintenance of genome integrity. Here, we identify a regulatory pathway that promotes stalled forks recovery from replication stress. We show that the mammalian replisome component C20orf43/RTF2 (homologous to S. pombe Rtf2) must be removed for fork restart to be optimal. We further show that the proteasomal shuttle proteins DDI1 and DDI2 are required for RTF2 removal from stalled forks. Persistence of RTF2 at stalled forks results in fork restart defects, hyperactivation of the DNA damage signal, accumulation of single-stranded DNA (ssDNA), sensitivity to replication drugs, and chromosome instability. These results establish that RTF2 removal is a key determinant for the ability of cells to manage replication stress and maintain genome integrity.

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Crossref · 10.1016/j.molcel.2017.11.035

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  • In S. Pombe, removal of RTFDC1 (RTF2) from stalled replication forks during S phase DNA replication is essential to maintain replication stress and genome integrity.

    “What is known to date is that in S. Pombe the removal of RTFDC1 (also known as RTF2) from stalled replication forks during S phase DNA replication is essential to maintain replication stress and genome integrity69.”

    From Variant-to-function mapping of late-onset Alzheimer’s disease GWAS signals in human microglial cell models implicates <i>RTFDC1</i> at the <i>CASS4</i> locus (2024) · cites this paper as [69]

    The Abstract and Discussion identify removal of RTF2 from stalled forks as a protective process in mammalian or human cells, not S. pombe. The Results section on DDI1/2 instead says S. pombe Rtf2 is required to maintain fork stalling at a specific replication termination site. Page numbers were not provided. (LLM, conf=0.87)

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Research works printed but not linked: 56

  1. Acs K, Luijsterburg MS, Ackermann L, Salomons FA, Hoppe T, and Dantuma NP (2011). The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks. Nat Struct Mol Biol 18, 1345– 1350. 22120668
  2. Alabert C, Bukowski-Wills JC, Lee SB, Kustatscher G, Nakamura K, de Lima Alves F, Menard P, Mejlvang J, Rappsilber J, and Groth A (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nat Cell Biol 16, 281– 293. 24561620 PMC4283098
  3. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, (2012). The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603– 607. 22460905 PMC3320027
  4. Bass TE, Luzwick JW, Kavanaugh G, Carroll C, Dungrawala H, Glick GG, Feldkamp MD, Putney R, Chazin WJ, and Cortez D (2016). ETAA1 acts at stalled replication forks to maintain genome integrity. Nat Cell Biol 18, 1185– 1195. 27723720 PMC5245861
  5. Branzei D, and Foiani M (2009). The checkpoint response to replication stress. DNA Repair (Amst) 8, 1038– 1046. 19482564
  6. Byun TS, Pacek M, Yee MC, Walter JC, and Cimprich KA (2005). Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint. Genes Dev 19, 1040– 1052. 15833913 PMC1091739
  7. Cho WH, Kang YH, An YY, Tappin I, Hurwitz J, and Lee JK (2013). Human Tim-Tipin complex affects the biochemical properties of the replicative DNA helicase and DNA polymerases. Proc Natl Acad Sci U S A 110, 2523– 2527. 23359676 PMC3574903
  8. Chou DM, and Elledge SJ (2006). Tipin and Timeless form a mutually protective complex required for genotoxic stress resistance and checkpoint function. Proc Natl Acad Sci U S A 103, 18143– 18147. 17116885 PMC1654129
  9. Consortium GT (2013). The Genotype-Tissue Expression (GTEx) project. Nat Genet 45, 580– 585. 23715323 PMC4010069
  10. Costanzo V, Shechter D, Lupardus PJ, Cimprich KA, Gottesman M, and Gautier J (2003). An ATR- and Cdc7-dependent DNA damage checkpoint that inhibits initiation of DNA replication. Mol Cell 11, 203– 213. 12535533
  11. Dantuma NP, Heinen C, and Hoogstraten D (2009). The ubiquitin receptor Rad23: at the crossroads of nucleotide excision repair and proteasomal degradation. DNA Repair (Amst) 8, 449– 460. 19223247
  12. De Piccoli G, Katou Y, Itoh T, Nakato R, Shirahige K, and Labib K (2012). Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases. Mol Cell 45, 696– 704. 22325992
  13. Dungrawala H, Rose KL, Bhat KP, Mohni KN, Glick GG, Couch FB, and Cortez D (2015). The Replication Checkpoint Prevents Two Types of Fork Collapse without Regulating Replisome Stability. Mol Cell 59, 998– 1010. 26365379 PMC4575883
  14. Elsasser S, Gali RR, Schwickart M, Larsen CN, Leggett DS, Muller B, Feng MT, Tubing F, Dittmar GA, and Finley D (2002). Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat Cell Biol 4, 725– 730. 12198498
  15. Errico A, Costanzo V, and Hunt T (2007). Tipin is required for stalled replication forks to resume DNA replication after removal of aphidicolin in Xenopus egg extracts. Proc Natl Acad Sci U S A 104, 14929– 14934. 17846426 PMC1975688
  16. Franz A, Ackermann L, and Hoppe T (2016). Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin. Front Genet 7, 73. 27200082 PMC4853748
  17. Friedel AM, Pike BL, and Gasser SM (2009). ATR/Mec1: coordinating fork stability and repair. Curr Opin Cell Biol 21, 237– 244. 19230642
  18. Gomez TA, Kolawa N, Gee M, Sweredoski MJ, and Deshaies RJ (2011). Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1. BMC Biol 9, 33. 21627799 PMC3126750
  19. Gotter AL, Suppa C, and Emanuel BS (2007). Mammalian TIMELESS and Tipin are evolutionarily conserved replication fork-associated factors. J Mol Biol 366, 36– 52. 17141802 PMC4151250
  20. Haahr P, Hoffmann S, Tollenaere MA, Ho T, Toledo LI, Mann M, Bekker-Jensen S, Raschle M, and Mailand N (2016). Activation of the ATR kinase by the RPA-binding protein ETAA1. Nat Cell Biol 18, 1196– 1207. 27723717
  21. Hamperl S, and Cimprich KA (2016). Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell 167, 1455– 1467. 27912056 PMC5141617
  22. Hashimoto Y, Ray Chaudhuri A, Lopes M, and Costanzo V (2010). Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat Struct Mol Biol 17, 1305– 1311. 20935632 PMC4306207
  23. He J, Zhu Q, Wani G, Sharma N, Han C, Qian J, Pentz K, Wang QE, and Wani AA (2014). Ubiquitin-specific protease 7 regulates nucleotide excision repair through deubiquitinating XPC protein and preventing XPC protein from undergoing ultraviolet light-induced and VCP/p97 protein-regulated proteolysis. J Biol Chem 289, 27278– 27289. 25118285 PMC4175359
  24. Hills SA, and Diffley JF (2014). DNA replication and oncogene-induced replicative stress. Curr Biol 24, R435– 444. 24845676
  25. Huang P, Chubb S, Hertel LW, Grindey GB, and Plunkett W (1991). Action of 2′,2′-difluorodeoxycytidine on DNA synthesis. Cancer Res 51, 6110– 6117. 1718594
  26. Inagawa T, Yamada-Inagawa T, Eydmann T, Mian IS, Wang TS, and Dalgaard JZ (2009). Schizosaccharomyces pombe Rtf2 mediates site-specific replication termination by inhibiting replication restart. Proc Natl Acad Sci U S A 106, 7927– 7932. 19416828 PMC2683088
  27. Kang Y, Vossler RA, Diaz-Martinez LA, Winter NS, Clarke DJ, and Walters KJ (2006). UBL/UBA ubiquitin receptor proteins bind a common tetraubiquitin chain. J Mol Biol 356, 1027– 1035. 16405905
  28. Kim JC, Harris ST, Dinter T, Shah KA, and Mirkin SM (2016). The role of break-induced replication in large-scale expansions of (CAG)n/(CTG)n repeats. Nat Struct Mol Biol. PMC5215974 27918542
  29. Kolinjivadi AM, Sannino V, De Antoni A, Zadorozhny K, Kilkenny M, Techer H, Baldi G, Shen R, Ciccia A, Pellegrini L, (2017). Smarcal1-Mediated Fork Reversal Triggers Mre11-Dependent Degradation of Nascent DNA in the Absence of Brca2 and Stable Rad51 Nucleofilaments. Mol Cell 67, 867– 881 e867. 28757209 PMC5594205
  30. Lambert S, and Carr AM (2013). Replication stress and genome rearrangements: lessons from yeast models. Curr Opin Genet Dev 23, 132– 139. 23267817
  31. Lee JA, Carvalho CM, and Lupski JR (2007). A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235– 1247. 18160035
  32. Leman AR, Noguchi C, Lee CY, and Noguchi E (2010). Human Timeless and Tipin stabilize replication forks and facilitate sister-chromatid cohesion. J Cell Sci 123, 660– 670. 20124417 PMC2823575
  33. Macheret M, and Halazonetis TD (2015). DNA replication stress as a hallmark of cancer. Annu Rev Pathol 10, 425– 448. 25621662
  34. Marini F, Nardo T, Giannattasio M, Minuzzo M, Stefanini M, Plevani P, and Muzi Falconi M (2006). DNA nucleotide excision repair-dependent signaling to checkpoint activation. Proc Natl Acad Sci U S A 103, 17325– 17330. 17088560 PMC1859929
  35. Mijic S, Zellweger R, Chappidi N, Berti M, Jacobs K, Mutreja K, Ursich S, Ray Chaudhuri A, Nussenzweig A, Janscak P, (2017). Replication fork reversal triggers fork degradation in BRCA2-defective cells. Nat Commun 8, 859. 29038466 PMC5643541
  36. Minocherhomji S, Ying S, Bjerregaard VA, Bursomanno S, Aleliunaite A, Wu W, Mankouri HW, Shen H, Liu Y, and Hickson ID (2015). Replication stress activates DNA repair synthesis in mitosis. Nature 528, 286– 290. 26633632
  37. Morawe T, Honemann-Capito M, von Stein W, and Wodarz A (2011). Loss of the extraproteasomal ubiquitin receptor Rings lost impairs ring canal growth in Drosophila oogenesis. J Cell Biol 193, 71– 80. 21444692 PMC3082182
  38. Neelsen KJ, Chaudhuri AR, Follonier C, Herrador R, and Lopes M (2014). Visualization and interpretation of eukaryotic DNA replication intermediates in vivo by electron microscopy. Methods Mol Biol 1094, 177– 208. 24162989
  39. Nowicka U, Zhang D, Walker O, Krutauz D, Castaneda CA, Chaturvedi A, Chen TY, Reis N, Glickman MH, and Fushman D (2015). DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Structure 23, 542– 557. 25703377 PMC4448915
  40. Ohashi M, Taguchi T, and Ikegami S (1978). Aphidicolin: a specific inhibitor of DNA polymerases in the cytosol of rat liver. Biochem Biophys Res Commun 82, 1084– 1090. 81050
  41. Ruthemann P, Balbo Pogliano C, and Naegeli H (2016). Global-genome Nucleotide Excision Repair Controlled by Ubiquitin/Sumo Modifiers. Front Genet 7, 68. 27200078 PMC4848295
  42. Schlacher K, Christ N, Siaud N, Egashira A, Wu H, and Jasin M (2011). Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell 145, 529– 542. 21565612 PMC3261725
  43. Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, and Cortez D (2013). Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. J Biol Chem 288, 31458– 31467. 24047897 PMC3814742
  44. Sirkis R, Gerst JE, and Fass D (2006). Ddi1, a eukaryotic protein with the retroviral protease fold. J Mol Biol 364, 376– 387. 17010377
  45. Siva M, Svoboda M, Veverka V, Trempe JF, Hofmann K, Kozisek M, Hexnerova R, Sedlak F, Belza J, Brynda J, (2016). Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog. Sci Rep 6, 30443. 27461074 PMC4962041
  46. Smith KD, Fu MA, and Brown EJ (2009). Tim-Tipin dysfunction creates an indispensible reliance on the ATR-Chk1 pathway for continued DNA synthesis. J Cell Biol 187, 15– 23. 19805627 PMC2762102
  47. Taglialatela A, Alvarez S, Leuzzi G, Sannino V, Ranjha L, Huang JW, Madubata C, Anand R, Levy B, Rabadan R, (2017). Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers. Mol Cell 68, 414– 430 e418. 29053959 PMC5720682
  48. Tang JY, Hwang BJ, Ford JM, Hanawalt PC, and Chu G (2000). Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis. Mol Cell 5, 737– 744. 10882109 PMC2894271
  49. Toledo LI, Altmeyer M, Rask MB, Lukas C, Larsen DH, Povlsen LK, Bekker-Jensen S, Mailand N, Bartek J, and Lukas J (2013). ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 155, 1088– 1103. 24267891
  50. Trempe JF, Saskova KG, Siva M, Ratcliffe CD, Veverka V, Hoegl A, Menade M, Feng X, Shenker S, Svoboda M, (2016). Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family. Sci Rep 6, 33671. 27646017 PMC5028754
  51. Unsal-Kacmaz K, Mullen TE, Kaufmann WK, and Sancar A (2005). Coupling of human circadian and cell cycles by the timeless protein. Mol Cell Biol 25, 3109– 3116. 15798197 PMC1069621
  52. van den Boom J, Wolf M, Weimann L, Schulze N, Li F, Kaschani F, Riemer A, Zierhut C, Kaiser M, Iliakis G, (2016). VCP/p97 Extracts Sterically Trapped Ku70/80 Rings from DNA in Double-Strand Break Repair. Mol Cell 64, 189– 198. 27716483 PMC5161236
  53. Willis NA, Chandramouly G, Huang B, Kwok A, Follonier C, Deng C, and Scully R (2014). BRCA1 controls homologous recombination at Tus/Ter-stalled mammalian replication forks. Nature 510, 556– 559. 24776801 PMC4118467
  54. Yoshizawa-Sugata N, and Masai H (2007). Human Tim/Timeless-interacting protein, Tipin, is required for efficient progression of S phase and DNA replication checkpoint. J Biol Chem 282, 2729– 2740. 17102137
  55. Zellweger R, Dalcher D, Mutreja K, Berti M, Schmid JA, Herrador R, Vindigni A, and Lopes M (2015). Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells. J Cell Biol 208, 563– 579. 25733714 PMC4347635
  56. Zhang F, Khajavi M, Connolly AM, Towne CF, Batish SD, and Lupski JR (2009). The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 41, 849– 853. 19543269 PMC4461229

Cited by

Sorted by citations

Authors
Kottemann, M. C., Conti, B. A., Lach, F. P., & Smogorzewska, A.
Affiliations
Rockefeller University (US)
Corresponding author
Smogorzewska, Agata
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2018-01
Volume
69
Issue
1
Pages
24-35.e5
ISSN
1097-2765 (ISSN-L)
OpenAlex
W2776494444
Cited by
49
References
7
Citations by year
2026: 2 · 2025: 2 · 2024: 8 · 2023: 7 · 2022: 6 · 2021: 4 · 2020: 13 · 2019: 4 · 2018: 3
FWCI
2.18
Type
journal article
Language
en
Open access
Locations
  • Molecular Cell (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Rockefeller University
  • American Cancer Society
  • NIH (#GM066699)
  • Pershing Square Sohn Prize for Young Investigators in Cancer Research
  • The Gabrielle H. Reem and Herbert J. Kayden Early-Career Innovation Award
  • HHMI
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords
replication fork restart, stalled replication forks, replisome, replication stress, genome stability, proteasome, Ddi1, DDI2, DNA damage response, single-stranded DNA, chromosomal instability
MeSH terms
Cell Cycle, DNA, DNA Damage, DNA Repair, DNA Replication, DNA-Binding Proteins, DNA, Single-Stranded, HeLa Cells, Humans, Stress, Physiological, Replication Origin, Cell Cycle Proteins, RNA Interference, RNA, Small Interfering, Genomic Instability, Cell Line, Tumor, Aspartic Acid Proteases

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