Structural basis of human PCNA sliding on DNA.

Abstract:

:Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residues within the ring channel, arranged in a right-hand spiral that matches the pitch of B-DNA. We propose that PCNA slides by tracking the DNA backbone via a 'cogwheel' mechanism based on short-lived polar interactions, which keep the orientation of the clamp invariant relative to DNA. Mutation of residues at the PCNA-DNA interface has been shown to impair the initiation of DNA synthesis by polymerase δ (pol δ). Therefore, our findings suggest that a clamp correctly oriented on DNA is necessary for the assembly of a replication-competent PCNA-pol δ holoenzyme.

journal_name

Nat Commun

journal_title

Nature communications

authors

De March M,Merino N,Barrera-Vilarmau S,Crehuet R,Onesti S,Blanco FJ,De Biasio A

doi

10.1038/ncomms13935

subject

Has Abstract

pub_date

2017-01-10 00:00:00

pages

13935

issn

2041-1723

pii

ncomms13935

journal_volume

8

pub_type

杂志文章
  • Circuit quantum acoustodynamics with surface acoustic waves.

    abstract::The experimental investigation of quantum devices incorporating mechanical resonators has opened up new frontiers in the study of quantum mechanics at a macroscopic level. It has recently been shown that surface acoustic waves (SAWs) can be piezoelectrically coupled to superconducting qubits, and confined in high-qual...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01063-9

    authors: Manenti R,Kockum AF,Patterson A,Behrle T,Rahamim J,Tancredi G,Nori F,Leek PJ

    更新日期:2017-10-17 00:00:00

  • Core-shell nanoscale coordination polymers combine chemotherapy and photodynamic therapy to potentiate checkpoint blockade cancer immunotherapy.

    abstract::Advanced colorectal cancer is one of the deadliest cancers, with a 5-year survival rate of only 12% for patients with the metastatic disease. Checkpoint inhibitors, such as the antibodies inhibiting the PD-1/PD-L1 axis, are among the most promising immunotherapies for patients with advanced colon cancer, but their dur...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12499

    authors: He C,Duan X,Guo N,Chan C,Poon C,Weichselbaum RR,Lin W

    更新日期:2016-08-17 00:00:00

  • Epigenetic engineering reveals a balance between histone modifications and transcription in kinetochore maintenance.

    abstract::Centromeres consist of specialized centrochromatin containing CENP-A nucleosomes intermingled with H3 nucleosomes carrying transcription-associated modifications. We have designed a novel synthetic biology 'in situ epistasis' analysis in which H3 dimethylated on lysine 4 (H3K4me2) demethylase LSD2 plus synthetic modul...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13334

    authors: Molina O,Vargiu G,Abad MA,Zhiteneva A,Jeyaprakash AA,Masumoto H,Kouprina N,Larionov V,Earnshaw WC

    更新日期:2016-11-14 00:00:00

  • Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA.

    abstract::Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability. Although molecular mechanisms of transcriptional bursting have ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13788

    authors: Fujita K,Iwaki M,Yanagida T

    更新日期:2016-12-07 00:00:00

  • Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility.

    abstract::Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid c...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03082-6

    authors: Behera V,Evans P,Face CJ,Hamagami N,Sankaranarayanan L,Keller CA,Giardine B,Tan K,Hardison RC,Shi J,Blobel GA

    更新日期:2018-02-22 00:00:00

  • Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition.

    abstract::Helitrons are eukaryotic DNA transposons that have profoundly affected genome variability via capture and mobilization of host genomic sequences. Defining their mode of action is therefore important for understanding how genome landscapes evolve. Sequence similarities with certain prokaryotic mobile elements suggest a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03688-w

    authors: Grabundzija I,Hickman AB,Dyda F

    更新日期:2018-03-29 00:00:00

  • The evolutionary origin of human hyper-cooperation.

    abstract::Proactive, that is, unsolicited, prosociality is a key component of our hyper-cooperation, which in turn has enabled the emergence of various uniquely human traits, including complex cognition, morality and cumulative culture and technology. However, the evolutionary foundation of the human prosocial sentiment remains...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5747

    authors: Burkart JM,Allon O,Amici F,Fichtel C,Finkenwirth C,Heschl A,Huber J,Isler K,Kosonen ZK,Martins E,Meulman EJ,Richiger R,Rueth K,Spillmann B,Wiesendanger S,van Schaik CP

    更新日期:2014-08-27 00:00:00

  • Energy-temperature uncertainty relation in quantum thermodynamics.

    abstract::It is known that temperature estimates of macroscopic systems in equilibrium are most precise when their energy fluctuations are large. However, for nanoscale systems deviations from standard thermodynamics arise due to their interactions with the environment. Here we include such interactions and, using quantum estim...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-04536-7

    authors: Miller HJD,Anders J

    更新日期:2018-06-06 00:00:00

  • Are microtubules tension sensors?

    abstract::Mechanical signals play many roles in cell and developmental biology. Several mechanotransduction pathways have been uncovered, but the mechanisms identified so far only address the perception of stress intensity. Mechanical stresses are tensorial in nature, and thus provide dual mechanical information: stress magnitu...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/s41467-019-10207-y

    authors: Hamant O,Inoue D,Bouchez D,Dumais J,Mjolsness E

    更新日期:2019-05-29 00:00:00

  • Cretaceous stem chondrichthyans survived the end-Permian mass extinction.

    abstract::Cladodontomorph sharks are Palaeozoic stem chondrichthyans thought to go extinct at the end-Permian mass extinction. This extinction preceded the diversification of euselachians, including modern sharks. Here we describe an outer-platform cladodontomorph shark tooth assemblage from the Early Cretaceous of southern Fra...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3669

    authors: Guinot G,Adnet S,Cavin L,Cappetta H

    更新日期:2013-01-01 00:00:00

  • DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress.

    abstract::Chemical modifications on DNA molecules, such as 5-methylcytosine and 5-hydroxymethylcytosine, play important roles in the mammalian brain. A novel DNA adenine modification, N(6)-methyladenine (6mA), has recently been found in mammalian cells. However, the presence and function(s) of 6mA in the mammalian brain remain ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-01195-y

    authors: Yao B,Cheng Y,Wang Z,Li Y,Chen L,Huang L,Zhang W,Chen D,Wu H,Tang B,Jin P

    更新日期:2017-10-24 00:00:00

  • Direct electrical quantification of glucose and asparagine from bodily fluids using nanopores.

    abstract::Crucial steps in the miniaturisation of biosensors are the conversion of a biological signal into an electrical current as well as the direct sampling of bodily fluids. Here we show that protein sensors in combination with a nanopore, acting as an electrical transducer, can accurately quantify metabolites in real time...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-06534-1

    authors: Galenkamp NS,Soskine M,Hermans J,Wloka C,Maglia G

    更新日期:2018-10-05 00:00:00

  • Repeated growth and bubbling transfer of graphene with millimetre-size single-crystal grains using platinum.

    abstract::Large single-crystal graphene is highly desired and important for the applications of graphene in electronics, as grain boundaries between graphene grains markedly degrade its quality and properties. Here we report the growth of millimetre-sized hexagonal single-crystal graphene and graphene films joined from such gra...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1702

    authors: Gao L,Ren W,Xu H,Jin L,Wang Z,Ma T,Ma LP,Zhang Z,Fu Q,Peng LM,Bao X,Cheng HM

    更新日期:2012-02-28 00:00:00

  • Genotoxic stress-triggered β-catenin/JDP2/PRMT5 complex facilitates reestablishing glutathione homeostasis.

    abstract::The mechanisms underlying how cells subjected to genotoxic stress reestablish reduction-oxidation (redox) homeostasis to scavenge genotoxic stress-induced reactive oxygen species (ROS), which maintains the physiological function of cellular processes and cell survival, remain unclear. Herein, we report that, via a TCF...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11696-7

    authors: Cao L,Wu G,Zhu J,Tan Z,Shi D,Wu X,Tang M,Li Z,Hu Y,Zhang S,Yu R,Mo S,Wu J,Song E,Li M,Song L,Li J

    更新日期:2019-08-21 00:00:00

  • Spatial expression analyses of the putative oncogene ciRS-7 in cancer reshape the microRNA sponge theory.

    abstract::Circular RNAs (circRNAs) have recently gained substantial attention in the cancer research field where most, including the putative oncogene ciRS-7 (CDR1as), have been proposed to function as competitive endogenous RNAs (ceRNAs) by sponging specific microRNAs. Here, we report the first spatially resolved cellular expr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18355-2

    authors: Kristensen LS,Ebbesen KK,Sokol M,Jakobsen T,Korsgaard U,Eriksen AC,Hansen TB,Kjems J,Hager H

    更新日期:2020-09-11 00:00:00

  • Chiral optical response of planar and symmetric nanotrimers enabled by heteromaterial selection.

    abstract::Chirality is an intriguing property of certain molecules, materials or artificial nanostructures, which allows them to interact with the spin angular momentum of the impinging light field. Due to their chiral geometry, they can distinguish between left- and right-hand circular polarization states or convert them into ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13117

    authors: Banzer P,Woźniak P,Mick U,De Leon I,Boyd RW

    更新日期:2016-10-13 00:00:00

  • Author Correction: A standard for near-scarless plasmid construction using reusable DNA parts.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature communications

    pub_type: 已发布勘误

    doi:10.1038/s41467-019-11859-6

    authors: Ma X,Liang H,Cui X,Liu Y,Lu H,Ning W,Poon NY,Ho B,Zhou K

    更新日期:2019-08-21 00:00:00

  • Clouds enhance Greenland ice sheet meltwater runoff.

    abstract::The Greenland ice sheet has become one of the main contributors to global sea level rise, predominantly through increased meltwater runoff. The main drivers of Greenland ice sheet runoff, however, remain poorly understood. Here we show that clouds enhance meltwater runoff by about one-third relative to clear skies, us...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10266

    authors: Van Tricht K,Lhermitte S,Lenaerts JT,Gorodetskaya IV,L'Ecuyer TS,Noël B,van den Broeke MR,Turner DD,van Lipzig NP

    更新日期:2016-01-12 00:00:00

  • Leukocyte integrin Mac-1 regulates thrombosis via interaction with platelet GPIbα.

    abstract::Inflammation and thrombosis occur together in many diseases. The leukocyte integrin Mac-1 (also known as integrin αMβ2, or CD11b/CD18) is crucial for leukocyte recruitment to the endothelium, and Mac-1 engagement of platelet GPIbα is required for injury responses in diverse disease models. However, the role of Mac-1 i...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15559

    authors: Wang Y,Gao H,Shi C,Erhardt PW,Pavlovsky A,A Soloviev D,Bledzka K,Ustinov V,Zhu L,Qin J,Munday AD,Lopez J,Plow E,Simon DI

    更新日期:2017-05-30 00:00:00

  • Serial processing of kinematic signals by cerebellar circuitry during voluntary whisking.

    abstract::Purkinje cells (PCs) in Crus 1 represent whisker movement via linear changes in firing rate, but the circuit mechanisms underlying this coding scheme are unknown. Here we examine the role of upstream inputs to PCs-excitatory granule cells (GCs) and inhibitory molecular layer interneurons-in processing of whisking sign...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00312-1

    authors: Chen S,Augustine GJ,Chadderton P

    更新日期:2017-08-10 00:00:00

  • Life cycle assessment needs predictive spatial modelling for biodiversity and ecosystem services.

    abstract::International corporations in an increasingly globalized economy exert a major influence on the planet's land use and resources through their product design and material sourcing decisions. Many companies use life cycle assessment (LCA) to evaluate their sustainability, yet commonly-used LCA methodologies lack the spa...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15065

    authors: Chaplin-Kramer R,Sim S,Hamel P,Bryant B,Noe R,Mueller C,Rigarlsford G,Kulak M,Kowal V,Sharp R,Clavreul J,Price E,Polasky S,Ruckelshaus M,Daily G

    更新日期:2017-04-21 00:00:00

  • Publisher Correction: MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-020-16538-5

    authors: Mattesen TB,Rasmussen MH,Sandoval J,Ongen H,Árnadóttir SS,Gladov J,Martinez-Cardus A,de Moura MC,Madsen AH,Laurberg S,Dermitzakis ET,Esteller M,Andersen CL,Bramsen JB

    更新日期:2020-06-03 00:00:00

  • The footprint of column collapse regimes on pyroclastic flow temperatures and plume heights.

    abstract::The gravitational collapse of eruption columns generates ground-hugging pyroclastic density currents (PDCs) with highly variable temperatures, high enough to be a threat for communities surrounding volcanoes. The reasons for such great temperature variability are debated in terms of eruptive versus transport and empla...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10337-3

    authors: Trolese M,Cerminara M,Esposti Ongaro T,Giordano G

    更新日期:2019-06-06 00:00:00

  • Quantum vertex model for reversible classical computing.

    abstract::Mappings of classical computation onto statistical mechanics models have led to remarkable successes in addressing some complex computational problems. However, such mappings display thermodynamic phase transitions that may prevent reaching solution even for easy problems known to be solvable in polynomial time. Here ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15303

    authors: Chamon C,Mucciolo ER,Ruckenstein AE,Yang ZC

    更新日期:2017-05-12 00:00:00

  • Information processing using a single dynamical node as complex system.

    abstract::Novel methods for information processing are highly desired in our information-driven society. Inspired by the brain's ability to process information, the recently introduced paradigm known as 'reservoir computing' shows that complex networks can efficiently perform computation. Here we introduce a novel architecture ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1476

    authors: Appeltant L,Soriano MC,Van der Sande G,Danckaert J,Massar S,Dambre J,Schrauwen B,Mirasso CR,Fischer I

    更新日期:2011-09-13 00:00:00

  • Quantum speedup in the identification of cause-effect relations.

    abstract::The ability to identify cause-effect relations is an essential component of the scientific method. The identification of causal relations is generally accomplished through statistical trials where alternative hypotheses are tested against each other. Traditionally, such trials have been based on classical statistics. ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09383-8

    authors: Chiribella G,Ebler D

    更新日期:2019-04-01 00:00:00

  • Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast.

    abstract::Rosemary extracts containing the phenolic diterpenes carnosic acid and its derivative carnosol are approved food additives used in an increasingly wide range of products to enhance shelf-life, thanks to their high anti-oxidant activity. We describe here the elucidation of the complete biosynthetic pathway of carnosic ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12942

    authors: Scheler U,Brandt W,Porzel A,Rothe K,Manzano D,Božić D,Papaefthimiou D,Balcke GU,Henning A,Lohse S,Marillonnet S,Kanellis AK,Ferrer A,Tissier A

    更新日期:2016-10-05 00:00:00

  • The structure of Zika virus NS5 reveals a conserved domain conformation.

    abstract::The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alterna...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14763

    authors: Wang B,Tan XF,Thurmond S,Zhang ZM,Lin A,Hai R,Song J

    更新日期:2017-03-27 00:00:00

  • Targeting stromal remodeling and cancer stem cell plasticity overcomes chemoresistance in triple negative breast cancer.

    abstract::The cellular and molecular basis of stromal cell recruitment, activation and crosstalk in carcinomas is poorly understood, limiting the development of targeted anti-stromal therapies. In mouse models of triple negative breast cancer (TNBC), Hedgehog ligand produced by neoplastic cells reprograms cancer-associated fibr...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05220-6

    authors: Cazet AS,Hui MN,Elsworth BL,Wu SZ,Roden D,Chan CL,Skhinas JN,Collot R,Yang J,Harvey K,Johan MZ,Cooper C,Nair R,Herrmann D,McFarland A,Deng N,Ruiz-Borrego M,Rojo F,Trigo JM,Bezares S,Caballero R,Lim E,Timpson P

    更新日期:2018-07-24 00:00:00

  • Efficient near-infrared up-conversion photoluminescence in carbon nanotubes.

    abstract::Photoluminescence phenomena normally obey Stokes' law of luminescence according to which the emitted photon energy is typically lower than its excitation counterparts. Here we show that carbon nanotubes break this rule under one-photon excitation conditions. We found that the carbon nanotubes exhibit efficient near-in...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9920

    authors: Akizuki N,Aota S,Mouri S,Matsuda K,Miyauchi Y

    更新日期:2015-11-16 00:00:00