Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting.

Abstract:

:Bacterial CRISPR-Cas systems comprise diverse effector endonucleases with different targeting ranges, specificities and enzymatic properties, but many of them are inactive in mammalian cells and are thus precluded from genome-editing applications. Here we show that the type II-B FnCas9 from Francisella novicida possesses novel properties, but its nuclease function is frequently inhibited at many genomic loci in living human cells. Moreover, we develop a proximal CRISPR (termed proxy-CRISPR) targeting method that restores FnCas9 nuclease activity in a target-specific manner. We further demonstrate that this proxy-CRISPR strategy is applicable to diverse CRISPR-Cas systems, including type II-C Cas9 and type V Cpf1 systems, and can facilitate precise gene editing even between identical genomic sites within the same genome. Our findings provide a novel strategy to enable use of diverse otherwise inactive CRISPR-Cas systems for genome-editing applications and a potential path to modulate the impact of chromatin microenvironments on genome modification.

journal_name

Nat Commun

journal_title

Nature communications

authors

Chen F,Ding X,Feng Y,Seebeck T,Jiang Y,Davis GD

doi

10.1038/ncomms14958

subject

Has Abstract

pub_date

2017-04-07 00:00:00

pages

14958

issn

2041-1723

pii

ncomms14958

journal_volume

8

pub_type

杂志文章
  • Evidence for the alkaline nature of parental carbonatite melts at Oka complex in Canada.

    abstract::The Earth's sole active carbonatite volcano, Oldoinyo Lengai (Tanzania), is presently erupting unique natrocarbonatite lavas that are characterized by Na- and K-bearing magmatic carbonates of nyerereite [Na2Ca(CO3)2] and gregoryite [(Na2,K2,Ca)CO3]. Contrarily, the vast majority of older, plutonic carbonatite occurren...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms3687

    authors: Chen W,Kamenetsky VS,Simonetti A

    更新日期:2013-01-01 00:00:00

  • Printable enzyme-embedded materials for methane to methanol conversion.

    abstract::An industrial process for the selective activation of methane under mild conditions would be highly valuable for controlling emissions to the environment and for utilizing vast new sources of natural gas. The only selective catalysts for methane activation and conversion to methanol under mild conditions are methane m...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms11900

    authors: Blanchette CD,Knipe JM,Stolaroff JK,DeOtte JR,Oakdale JS,Maiti A,Lenhardt JM,Sirajuddin S,Rosenzweig AC,Baker SE

    更新日期:2016-06-15 00:00:00

  • Pyroclastic passage zones in glaciovolcanic sequences.

    abstract::Volcanoes are increasingly recognized as agents and recorders of global climate variability, although deciphering the linkages between planetary climate and volcanism is still in its infancy. The growth and emergence of subaqueous volcanoes produce passage zones, which are stratigraphic surfaces marking major transiti...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2829

    authors: Russell JK,Edwards BR,Porritt LA

    更新日期:2013-01-01 00:00:00

  • A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females.

    abstract::Idiopathic scoliosis (IS) is a common paediatric musculoskeletal disease that displays a strong female bias. By performing a genome-wide association study (GWAS) of 3,102 individuals, we identify significant associations with 20p11.22 SNPs for females (P=6.89 × 10(-9)) but not males (P=0.71). This association with IS ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7452

    authors: Sharma S,Londono D,Eckalbar WL,Gao X,Zhang D,Mauldin K,Kou I,Takahashi A,Matsumoto M,Kamiya N,Murphy KK,Cornelia R,TSRHC Scoliosis Clinical Group.,Japan Scoliosis Clinical Research Group.,Herring JA,Burns D,Ahituv N,Ike

    更新日期:2015-03-18 00:00:00

  • STING-dependent paracriny shapes apoptotic priming of breast tumors in response to anti-mitotic treatment.

    abstract::A fascinating but uncharacterized action of antimitotic chemotherapy is to collectively prime cancer cells to apoptotic mitochondrial outer membrane permeabilization (MOMP), while impacting only on cycling cell subsets. Here, we show that a proapoptotic secretory phenotype is induced by activation of cGAS/STING in can...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13689-y

    authors: Lohard S,Bourgeois N,Maillet L,Gautier F,Fétiveau A,Lasla H,Nguyen F,Vuillier C,Dumont A,Moreau-Aubry A,Frapin M,David L,Loussouarn D,Kerdraon O,Campone M,Jézéquel P,Juin PP,Barillé-Nion S

    更新日期:2020-01-14 00:00:00

  • Standing genetic variation fuels rapid adaptation to ocean acidification.

    abstract::Global climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous global change stressor that is affecting marine ecosystems globally. Here, we quantify the phenotypic and genetic modifications ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13767-1

    authors: Bitter MC,Kapsenberg L,Gattuso JP,Pfister CA

    更新日期:2019-12-20 00:00:00

  • Meningeal lymphatic dysfunction exacerbates traumatic brain injury pathogenesis.

    abstract::Traumatic brain injury (TBI) is a leading global cause of death and disability. Here we demonstrate in an experimental mouse model of TBI that mild forms of brain trauma cause severe deficits in meningeal lymphatic drainage that begin within hours and last out to at least one month post-injury. To investigate a mechan...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18113-4

    authors: Bolte AC,Dutta AB,Hurt ME,Smirnov I,Kovacs MA,McKee CA,Ennerfelt HE,Shapiro D,Nguyen BH,Frost EL,Lammert CR,Kipnis J,Lukens JR

    更新日期:2020-09-10 00:00:00

  • The nasal methylome as a biomarker of asthma and airway inflammation in children.

    abstract::The nasal cellular epigenome may serve as biomarker of airway disease and environmental response. Here we collect nasal swabs from the anterior nares of 547 children (mean-age 12.9 y), and measure DNA methylation (DNAm) with the Infinium MethylationEPIC BeadChip. We perform nasal Epigenome-Wide Association analyses (E...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11058-3

    authors: Cardenas A,Sordillo JE,Rifas-Shiman SL,Chung W,Liang L,Coull BA,Hivert MF,Lai PS,Forno E,Celedón JC,Litonjua AA,Brennan KJ,DeMeo DL,Baccarelli AA,Oken E,Gold DR

    更新日期:2019-07-12 00:00:00

  • Regulation of PCNA cycling on replicating DNA by RFC and RFC-like complexes.

    abstract::Replication-Factor-C (RFC) and RFC-like complexes (RLCs) mediate chromatin engagement of the proliferating cell nuclear antigen (PCNA). It remains controversial how RFC and RLCs cooperate to regulate PCNA loading and unloading. Here, we show the distinct PCNA loading or unloading activity of each clamp loader. ATAD5-R...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10376-w

    authors: Kang MS,Ryu E,Lee SW,Park J,Ha NY,Ra JS,Kim YJ,Kim J,Abdel-Rahman M,Park SH,Lee KY,Kim H,Kang S,Myung K

    更新日期:2019-06-03 00:00:00

  • Severe NDE1-mediated microcephaly results from neural progenitor cell cycle arrests at multiple specific stages.

    abstract::Microcephaly is a cortical malformation disorder characterized by an abnormally small brain. Recent studies have revealed severe cases of microcephaly resulting from human mutations in the NDE1 gene, which is involved in the regulation of cytoplasmic dynein. Here using in utero electroporation of NDE1 short hairpin RN...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12551

    authors: Doobin DJ,Kemal S,Dantas TJ,Vallee RB

    更新日期:2016-08-24 00:00:00

  • Visualization of nanocrystal breathing modes at extreme strains.

    abstract::Nanoscale dimensions in materials lead to unique electronic and structural properties with applications ranging from site-specific drug delivery to anodes for lithium-ion batteries. These functional properties often involve large-amplitude strains and structural modifications, and thus require an understanding of the ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7577

    authors: Szilagyi E,Wittenberg JS,Miller TA,Lutker K,Quirin F,Lemke H,Zhu D,Chollet M,Robinson J,Wen H,Sokolowski-Tinten K,Lindenberg AM

    更新日期:2015-03-12 00:00:00

  • Polymorphism of dislocation core structures at the atomic scale.

    abstract::Dislocation defects together with their associated strain fields and segregated impurities are of considerable significance in many areas of materials science. However, their atomic-scale structures have remained extremely challenging to resolve, limiting our understanding of these ubiquitous defects. Here, by develop...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4239

    authors: Wang Z,Saito M,McKenna KP,Ikuhara Y

    更新日期:2014-01-01 00:00:00

  • Surface transfer doping induced effective modulation on ambipolar characteristics of few-layer black phosphorus.

    abstract::Black phosphorus, a fast emerging two-dimensional material, has been configured as field effect transistors, showing a hole-transport-dominated ambipolar characteristic. Here we report an effective modulation on ambipolar characteristics of few-layer black phosphorus transistors through in situ surface functionalizati...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms7485

    authors: Xiang D,Han C,Wu J,Zhong S,Liu Y,Lin J,Zhang XA,Ping Hu W,Özyilmaz B,Neto AH,Wee AT,Chen W

    更新日期:2015-03-12 00:00:00

  • Caloric restriction reduces age-related and all-cause mortality in rhesus monkeys.

    abstract::Caloric restriction (CR) without malnutrition increases longevity and delays the onset of age-associated disorders in short-lived species, from unicellular organisms to laboratory mice and rats. The value of CR as a tool to understand human ageing relies on translatability of CR's effects in primates. Here we show tha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4557

    authors: Colman RJ,Beasley TM,Kemnitz JW,Johnson SC,Weindruch R,Anderson RM

    更新日期:2014-04-01 00:00:00

  • Escape from nonsense-mediated decay associates with anti-tumor immunogenicity.

    abstract::Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific expression analysi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17526-5

    authors: Litchfield K,Reading JL,Lim EL,Xu H,Liu P,Al-Bakir M,Wong YNS,Rowan A,Funt SA,Merghoub T,Perkins D,Lauss M,Svane IM,Jönsson G,Herrero J,Larkin J,Quezada SA,Hellmann MD,Turajlic S,Swanton C

    更新日期:2020-07-30 00:00:00

  • Multiscale real time and high sensitivity ion detection with complementary organic electrochemical transistors amplifier.

    abstract::Ions are ubiquitous biological regulators playing a key role for vital processes in animals and plants. The combined detection of ion concentration and real-time monitoring of small variations with respect to the resting conditions is a multiscale functionality providing important information on health states. This mu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17547-0

    authors: Romele P,Gkoupidenis P,Koutsouras DA,Lieberth K,Kovács-Vajna ZM,Blom PWM,Torricelli F

    更新日期:2020-07-27 00:00:00

  • Author Correction: Designing minimal genomes using whole-cell models.

    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/s41467-020-15994-3

    authors: Rees-Garbutt J,Chalkley O,Landon S,Purcell O,Marucci L,Grierson C

    更新日期:2020-05-06 00:00:00

  • Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.

    abstract::To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large gen...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18630-2

    authors: Espah Borujeni A,Zhang J,Doosthosseini H,Nielsen AAK,Voigt CA

    更新日期:2020-10-05 00:00:00

  • Jouvence a small nucleolar RNA required in the gut extends lifespan in Drosophila.

    abstract::Longevity is influenced by genetic and environmental factors, but the underlying mechanisms remain elusive. Here, we functionally characterise a Drosophila small nucleolar RNA (snoRNA), named jouvence whose loss of function reduces lifespan. The genomic region of jouvence rescues the longevity in mutant, while its ove...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-14784-1

    authors: Soulé S,Mellottée L,Arab A,Chen C,Martin JR

    更新日期:2020-02-20 00:00:00

  • Iridates from the molecular side.

    abstract::New exotic phenomena have recently been discovered in oxides of paramagnetic Ir(4+) ions, widely known as 'iridates'. Their remarkable properties originate from concerted effects of the crystal field, magnetic interactions and strong spin-orbit coupling, characteristic of 5d metal ions. Despite numerous experimental r...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12195

    authors: Pedersen KS,Bendix J,Tressaud A,Durand E,Weihe H,Salman Z,Morsing TJ,Woodruff DN,Lan Y,Wernsdorfer W,Mathonière C,Piligkos S,Klokishner SI,Ostrovsky S,Ollefs K,Wilhelm F,Rogalev A,Clérac R

    更新日期:2016-07-20 00:00:00

  • Ecological constraints increase the climatic debt in forests.

    abstract::Biodiversity changes are lagging behind current climate warming. The underlying determinants of this climatic debt are unknown and yet critical to understand the impacts of climate change on the present biota and improve forecasts of biodiversity changes. Here we assess determinants of climatic debt accumulated in Fre...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12643

    authors: Bertrand R,Riofrío-Dillon G,Lenoir J,Drapier J,de Ruffray P,Gégout JC,Loreau M

    更新日期:2016-08-26 00:00:00

  • Surface regulation enables high stability of single-crystal lithium-ion cathodes at high voltage.

    abstract::Single-crystal cathode materials for lithium-ion batteries have attracted increasing interest in providing greater capacity retention than their polycrystalline counterparts. However, after being cycled at high voltages, these single-crystal materials exhibit severe structural instability and capacity fade. Understand...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16824-2

    authors: Zhang F,Lou S,Li S,Yu Z,Liu Q,Dai A,Cao C,Toney MF,Ge M,Xiao X,Lee WK,Yao Y,Deng J,Liu T,Tang Y,Yin G,Lu J,Su D,Wang J

    更新日期:2020-06-16 00:00:00

  • Optical patterning of trapped charge in nitrogen-doped diamond.

    abstract::The nitrogen-vacancy (NV) centre in diamond is emerging as a promising platform for solid-state quantum information processing and nanoscale metrology. Of interest in these applications is the manipulation of the NV charge, which can be attained by optical excitation. Here, we use two-colour optical microscopy to inve...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12660

    authors: Jayakumar H,Henshaw J,Dhomkar S,Pagliero D,Laraoui A,Manson NB,Albu R,Doherty MW,Meriles CA

    更新日期:2016-08-30 00:00:00

  • Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.

    abstract::Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolu...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17327-w

    authors: Chaguza C,Senghore M,Bojang E,Gladstone RA,Lo SW,Tientcheu PE,Bancroft RE,Worwui A,Foster-Nyarko E,Ceesay F,Okoi C,McGee L,Klugman KP,Breiman RF,Barer MR,Adegbola RA,Antonio M,Bentley SD,Kwambana-Adams BA

    更新日期:2020-07-10 00:00:00

  • Graphite-protected CsPbBr3 perovskite photoanodes functionalised with water oxidation catalyst for oxygen evolution in water.

    abstract::Metal-halide perovskites have been widely investigated in the photovoltaic sector due to their promising optoelectronic properties and inexpensive fabrication techniques based on solution processing. Here we report the development of inorganic CsPbBr3-based photoanodes for direct photoelectrochemical oxygen evolution ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10124-0

    authors: Poli I,Hintermair U,Regue M,Kumar S,Sackville EV,Baker J,Watson TM,Eslava S,Cameron PJ

    更新日期:2019-05-08 00:00:00

  • Understanding water's anomalies with locally favoured structures.

    abstract::Water is a complex liquid that displays a surprising array of unusual properties, the most famous being the density maximum at about 4 °C. The origin of these anomalies is still a matter of debate, and so far a quantitative description of water's phase behaviour starting from the molecular arrangements is still missin...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms4556

    authors: Russo J,Tanaka H

    更新日期:2014-04-02 00:00:00

  • LFA-1 activates focal adhesion kinases FAK1/PYK2 to generate LAT-GRB2-SKAP1 complexes that terminate T-cell conjugate formation.

    abstract::Lymphocyte function-associated antigen 1 (LFA-1) affinity and avidity changes have been assumed to mediate adhesion to intercellular adhesion molecule-1 for T-cell conjugation to dendritic cells (DC). Although the T-cell receptor (TCR) and LFA-1 can generate intracellular signals, the immune cell adaptor protein linke...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms16001

    authors: Raab M,Lu Y,Kohler K,Smith X,Strebhardt K,Rudd CE

    更新日期:2017-07-12 00:00:00

  • Tornado outbreak variability follows Taylor's power law of fluctuation scaling and increases dramatically with severity.

    abstract::Tornadoes cause loss of life and damage to property each year in the United States and around the world. The largest impacts come from 'outbreaks' consisting of multiple tornadoes closely spaced in time. Here we find an upward trend in the annual mean number of tornadoes per US tornado outbreak for the period 1954-201...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10668

    authors: Tippett MK,Cohen JE

    更新日期:2016-02-29 00:00:00

  • Single-shot spectro-temporal characterization of XUV pulses from a seeded free-electron laser.

    abstract::Intense ultrashort X-ray pulses produced by modern free-electron lasers (FELs) allow one to probe biological systems, inorganic materials and molecular reaction dynamics with nanoscale spatial and femtoscale temporal resolution. These experiments require the knowledge, and possibly the control, of the spectro-temporal...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9075

    authors: De Ninno G,Gauthier D,Mahieu B,Ribič PR,Allaria E,Cinquegrana P,Danailov MB,Demidovich A,Ferrari E,Giannessi L,Penco G,Sigalotti P,Stupar M

    更新日期:2015-08-20 00:00:00

  • Prophage-triggered membrane vesicle formation through peptidoglycan damage in Bacillus subtilis.

    abstract::Bacteria release membrane vesicles (MVs) that play important roles in various biological processes. However, the mechanisms of MV formation in Gram-positive bacteria are unclear, as these cells possess a single cytoplasmic membrane that is surrounded by a thick cell wall. Here we use live cell imaging and electron cry...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00492-w

    authors: Toyofuku M,Cárcamo-Oyarce G,Yamamoto T,Eisenstein F,Hsiao CC,Kurosawa M,Gademann K,Pilhofer M,Nomura N,Eberl L

    更新日期:2017-09-07 00:00:00