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| Open AccessRTF2 controls replication repriming and ribonucleotide excision at the replisome
Ribonucleotides are incorporated into DNA during every S phase. Here, the authors show that replisome protein RTF2 localizes RNase H2 to the replisome, promoting ribonucleotide removal by RNase H2 when replication is ongoing but interfering with PRIM1-dependent restart following fork stalling.
- Brooke A. Conti
- , Penelope D. Ruiz
- & Agata Smogorzewska
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Article
| Open AccessStructural basis for DNA proofreading
Here, the authors use cryo-EM to capture nine intermediates along the DNA proofreading pathway using human mitochondrial DNA Polymerase Gamma. The results provide a step-by-step view of the DNA proofreading at single-nucleotide resolution.
- Gina Buchel
- , Ashok R. Nayak
- & Dmitry Temiakov
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| Open AccessMolecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases
Family D replicative DNA polymerases (PolD) contain a unique proofreading active site. Here, the authors present structures of PolD and enzymatic studies, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading.
- Leonardo Betancurt-Anzola
- , Markel Martínez-Carranza
- & Ludovic Sauguet
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Article
| Open AccessTRAIP resolves DNA replication-transcription conflicts during the S-phase of unperturbed cells
The TRAIP E3 ubiquitin ligase is essential for genome integrity, mutations lead to primordial dwarfism in patients. Here, the authors show that TRAIP degradation in S-phase, results in cell arrest due to DNA damage caused by replication-transcription conflicts.
- Shaun Scaramuzza
- , Rebecca M. Jones
- & Agnieszka Gambus
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Article
| Open AccessStructural basis of the T4 bacteriophage primosome assembly and primer synthesis
Here the authors present a methodical cryo-EM analysis to show how a T4 bacteriophage gp41 helicase hexamer and a gp61 primase assemble with a template-primer into an active primosome.
- Xiang Feng
- , Michelle M. Spiering
- & Huilin Li
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Article
| Open AccessMolecular choreography of primer synthesis by the eukaryotic Pol α-primase
DNA Polymerase α has separate RNA and DNA Polymerase subunits to form a hybrid RNA-DNA primer of unique length. Cryo-EM structures of each stage in primer synthesis reveal large movements among the four subunits and explain how primer length may be limited.
- Zuanning Yuan
- , Roxana Georgescu
- & Michael E. O’Donnell
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Article
| Open AccessMitotic DNA synthesis in response to replication stress requires the sequential action of DNA polymerases zeta and delta in human cells
DNA replication stress can generate under-replicated DNA regions which is fixed by an atypical form of DNA repair synthesis in mitosis (MiDAS). Here the authors show that translesion and replicative DNA polymerases cooperate via the POLD3 subunit to complete MiDAS in human cells.
- Wei Wu
- , Szymon A. Barwacz
- & Ying Liu
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Article
| Open AccessCell division drives DNA methylation loss in late-replicating domains in primary human cells
DNA methylation loss has been observed in aging tissues and cancers for decades. Researchers from Van Andel Institute have now provided experimental evidence that this process is directly driven by cell division.
- Jamie L. Endicott
- , Paula A. Nolte
- & Peter W. Laird
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Article
| Open AccessSolving the MCM paradox by visualizing the scaffold of CMG helicase at active replisomes
For several decades the MCM2-7 proteins, the core of the DNA replicative helicase, eluded detection at DNA replication sites. Here, the authors solve this conundrum by gene editing, which enables visualization of replication dynamics in living cells.
- Hana Polasek-Sedlackova
- , Thomas C. R. Miller
- & Jiri Lukas
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Article
| Open AccessIn crystallo observation of three metal ion promoted DNA polymerase misincorporation
By observing DNA polymerase misincorporation with time-resolved crystallography, the authors visualize three-metal ion dependent polymerase catalysis and identify A-site metal-mediated primer alignment as a key step in nucleotide discrimination.
- Caleb Chang
- , Christie Lee Luo
- & Yang Gao
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Article
| Open AccessThe combined DNA and RNA synthetic capabilities of archaeal DNA primase facilitate primer hand-off to the replicative DNA polymerase
DNA primases initiate a short primer before handing off to DNA polymerases to continue replication. Here the authors reveal a unique ability of archaeal primases to first synthesize RNA before stochastically incorporating a deoxyribonucleotide and further extending the primer as DNA.
- Mark D. Greci
- , Joseph D. Dooher
- & Stephen D. Bell
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Article
| Open AccessThe RAD51 recombinase protects mitotic chromatin in human cells
RAD51 is a well known player of DNA repair and homologous recombination. Here the authors reveal a function for RAD51 in protecting under-replicated DNA in mitotic human cells, promoting mitotic DNA synthesis (MiDAS) and successful chromosome segregation.
- Isabel E. Wassing
- , Emily Graham
- & Fumiko Esashi
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Article
| Open AccessRNF168-mediated localization of BARD1 recruits the BRCA1-PALB2 complex to DNA damage
The BRCA1-PALB2-BRCA2-RAD51 (BRCA1-P) complex is well known to play a fundamental role in DNA repair, but how the complex recruitment is regulated is still a matter of interest. Here the authors reveal mechanistic insights into RNF168 activity being responsible for PALB2 recruitment, through BARD1-BRCA1 during homologous recombination repair.
- John J. Krais
- , Yifan Wang
- & Neil Johnson
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Article
| Open AccessMechanism of genome instability mediated by human DNA polymerase mu misincorporation
Pol μ performs gap-filling repair synthesis in the nonhomologous end joining (NHEJ) pathway. Here the authors provide crystal structures and kinetics of human Pol μ to reveal insights into the molecular mechanism of Pol μ during the process of dGTP misincorporation.
- Miao Guo
- , Yina Wang
- & Ye Zhao
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Article
| Open AccessMIF is a 3’ flap nuclease that facilitates DNA replication and promotes tumor growth
Replication stress is associated with cancer formation and progression. Here the authors reveal that the macrophage migration inhibitory factor (MIF) functions as 3’ flap nuclease involved in resolving replication stress affecting overall tumor progression.
- Yijie Wang
- , Yan Chen
- & Yingfei Wang
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Article
| Open AccessMechanism of MRX inhibition by Rif2 at telomeres
Different proteins localised at telomeres ensure chromosome end stability to prevent double strand-end break recognition. Here the authors provide new insight into how in S. cerevisiae the interaction between Rif2 and Rad50 inhibits MRX functions at telomeres.
- Florian Roisné-Hamelin
- , Sabrina Pobiega
- & Stéphane Marcand
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Article
| Open AccessStabilisation of half MCM ring by Cdt1 during DNA insertion
During pre-Replication Complex, eukaryotic cells load two MCMs into a head-to-head Double Hexamer around duplex DNA (DH). Here the authors preRC assembly assay with purified proteins to reveal insights into S. cerevisiae’s first steps that lead to the DH formation.
- Marina Guerrero-Puigdevall
- , Narcis Fernandez-Fuentes
- & Jordi Frigola
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Article
| Open AccessPolymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path
In high fidelity DNA polymerases the exonuclease site is distal from the polymerization site and it is unknown how the primer strand travels between the two sites when mis-incorporated nucleotides must be removed. Here, the authors perform MD simulations and identify an optimal path for DNA primer strand translocation in the E. coli replicative DNA polymerase III and characterise the kinetics and dynamics of the Pol III pol-to-exo mode transition, which is validated with mutagenesis experiments.
- Thomas Dodd
- , Margherita Botto
- & Ivaylo Ivanov
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Article
| Open AccessMechanisms of telomerase inhibition by oxidized and therapeutic dNTPs
Telomerase enzymes add telomeric repeats to the end of linear chromosomes. Here the authors reveal mechanisms by which oxidized dNTPs and therapeutic dNTPs inhibit telomerase-mediated telomere elongation.
- Samantha L. Sanford
- , Griffin A. Welfer
- & Patricia L. Opresko
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Article
| Open AccessCross-regulation of viral kinases with cyclin A secures shutoff of host DNA synthesis
Herpesviruses code for conserved protein kinases (CHPKs) that exert several regulatory functions by interacting with cellular factors. Here, the authors use affinity purification mass spectrometry (AP–MS) to identify differential interaction partners of CHPKs from seven different human herpesviruses, finding Cyclin A and associated factors as a specific signature of β-herpesvirus kinases.
- Boris Bogdanow
- , Max Schmidt
- & Lüder Wiebusch
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Article
| Open AccessWarsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion
WABS patient derived cells display loss of sister chromatid cohesion. Here the authors by analyzing WABS patient derived cells, reveal a role of the DDX11 helicase in resolving G-Quadruplex structures to support sister chromatid cohesion.
- Janne J. M. van Schie
- , Atiq Faramarz
- & Job de Lange
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Article
| Open AccessMolecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C
Mycobacteria Prim-PolC performs short gap synthesis following removal of lesions during excision repair. Here the authors resolve crystal structures of pre- and post-catalytic Prim-PolC complexes bound to gapped DNA substrates to define its mechanism.
- Nigel C. Brissett
- , Katerina Zabrady
- & Aidan J. Doherty
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Article
| Open AccessBRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage
In order to avoid transcription-replication conflicts (TRCs) on shared DNA templates, cell must maintain strict spatiotemporal co-ordination of transcription with replication. Here the authors uncover a role for BRD4 in preventing TRCs and DNA damage checkpoint signaling in oncogenic cells.
- Fred C. Lam
- , Yi Wen Kong
- & Michael B. Yaffe
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Article
| Open AccessE2F-dependent transcription determines replication capacity and S phase length
DNA replication is tightly regulated during S phase of the cell cycle to ensure timely and accurate genome duplication. Here, the authors reveal that E2F-dependent transcription determines the maximal amount of DNA a cell is able to synthesise per unit time throughout S phase.
- Betheney R. Pennycook
- , Eva Vesela
- & Robertus A. M. de Bruin
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Article
| Open AccessStructure of the polymerase ε holoenzyme and atomic model of the leading strand replisome
DNA polymerase epsilon (Pol ε) is responsible for leading strand synthesis during DNA replication. Here the authors use Cryo-EM to describe the architecture of the Pol ε holoenzyme and to provide an atomic model for the leading strand replisome.
- Zuanning Yuan
- , Roxana Georgescu
- & Huilin Li
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Article
| Open AccessBudding yeast complete DNA synthesis after chromosome segregation begins
In the S phase of the cell cycle, the full genome needs to be replicated before cell division occurs. Here, authors show that in budding yeast DNA synthesis is completed after chromosome segregation begins.
- Tsvetomira Ivanova
- , Michael Maier
- & Manuel Mendoza
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Article
| Open AccessSSRP1-mediated histone H1 eviction promotes replication origin assembly and accelerated development
During embryonic development, it is vital to maintain rapid genome duplication. Here, the authors shed light on the mechanism by revealing that SSRP1 stimulates replication origin assembly on somatic nuclei in Xenopus laevis egg extract by promoting histone H1 eviction from somatic chromatin.
- Lucia Falbo
- , Erica Raspelli
- & Vincenzo Costanzo
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Article
| Open AccessDna2 processes behind the fork long ssDNA flaps generated by Pif1 and replication-dependent strand displacement
DNA2 encodes a 5′ flap DNA endonuclease involved in replication and DNA double strand break processing. Here the authors by using a conditional degron system together with electron microscopy characterize the role played by Dna2 and Pif1 helicase during unperturbed DNA replication in S. cerevisiae.
- Silvia Emma Rossi
- , Marco Foiani
- & Michele Giannattasio
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Article
| Open AccessDHX9 helicase promotes R-loop formation in cells with impaired RNA splicing
Unresolved R-loops can represent a threat to genome stability. Here the authors reveal that DHX9 helicase can promote R-loop formation in the absence of splicing factors SFPQ and SF3B3.
- Prasun Chakraborty
- , Jeffrey T. J. Huang
- & Kevin Hiom
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Article
| Open AccessEvidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae
DNA polymerases δ and ε (Pols δ and ε) are thought to be responsible for lagging and leading strand synthesis, respectively. Here the authors present evidence that Pol δ contributes to the initiation of leading strand replication in budding yeast by synthesizing DNA of both strands at replication origins.
- Marta A. Garbacz
- , Scott A. Lujan
- & Thomas A. Kunkel
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Article
| Open AccessPrimer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster
Primase is the specialised DNA-dependent RNA polymerase responsible for the initiation of DNA synthesis during DNA replication. Here the authors use a structural biology approach to identify the initiation site in the S. solfataricus PriSLX primase and to demonstrate that its Fe-S cluster is dispensable for primer synthesis.
- Sandro Holzer
- , Jiangyu Yan
- & Luca Pellegrini
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Article
| Open AccessATR inhibition facilitates targeting of leukemia dependence on convergent nucleotide biosynthetic pathways
Leukemic cells depend on the nucleotide synthesis pathway to proliferate. Here the authors use metabolomics and proteomics to show that inhibition of ATR reduced the activity of these pathways thus providing a valuable therapeutic target in leukemia.
- Thuc M. Le
- , Soumya Poddar
- & Caius G. Radu
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Article
| Open AccessIdentification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme
The current model for B-family DNA polymerases in archaea is one of single-subunit enzymes in contrast to the multi-subunit complexes in eukaryotes. Here the authors show that PolB1 fromSulfolobus solfataricusexists as a heterotrimeric complex in cell extracts.
- Jiangyu Yan
- , Thomas R. Beattie
- & Stephen D. Bell
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Article
| Open AccessDciA is an ancestral replicative helicase operator essential for bacterial replication initiation
DNA replication requires the loading of the replicative helicase onto the DNA molecule; in bacteria this was believed to be solely accomplished by DnaC and DnaI. Here the authors identify DciA as an ancestral and still widely distributed replicative helicase loader.
- Pierre Brézellec
- , Isabelle Vallet-Gely
- & Jean-Luc Ferat
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Article
| Open AccessCrosstalk between MSH2–MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair
The expansion of trinucleotide repeats can have detrimental effects and give rise to a range of human diseases. Here the authors report that the mismatch repair and the base excision repair machinery can operate together to promote expansion during lesion removal.
- Yanhao Lai
- , Helen Budworth
- & Yuan Liu
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Article |
Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds
Assembling defined sequences of DNA is important for many applications, but the synthesis becomes more difficult as the target size increases. Here, the authors report a method for assembling DNA by combining smaller strands, with the final structure determined by the order of addition of the fragments.
- Graham D. Hamblin
- , Janane F. Rahbani
- & Hanadi F. Sleiman