Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance.

Abstract:

:To fully exploit the microbial genome resources, a high-throughput experimental platform is needed to associate genes with phenotypes at the genome level. We present here a novel method that enables investigation of the cellular consequences of repressing individual transcripts based on the CRISPR interference (CRISPRi) pooled screening in bacteria. We identify rules for guide RNA library design to handle the unique structure of prokaryotic genomes by tiling screening and construct an E. coli genome-scale guide RNA library (~60,000 members) accordingly. We show that CRISPRi outperforms transposon sequencing, the benchmark method in the microbial functional genomics field, when similar library sizes are used or gene length is short. This tool is also effective for mapping phenotypes to non-coding RNAs (ncRNAs), as elucidated by a comprehensive tRNA-fitness map constructed here. Our results establish CRISPRi pooled screening as a powerful tool for mapping complex prokaryotic genetic networks in a precise and high-throughput manner.

journal_name

Nat Commun

journal_title

Nature communications

authors

Wang T,Guan C,Guo J,Liu B,Wu Y,Xie Z,Zhang C,Xing XH

doi

10.1038/s41467-018-04899-x

subject

Has Abstract

pub_date

2018-06-26 00:00:00

pages

2475

issue

1

issn

2041-1723

pii

10.1038/s41467-018-04899-x

journal_volume

9

pub_type

杂志文章
  • Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues.

    abstract::Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxyge...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12121

    authors: Tzoumas S,Nunes A,Olefir I,Stangl S,Symvoulidis P,Glasl S,Bayer C,Multhoff G,Ntziachristos V

    更新日期:2016-06-30 00:00:00

  • Polarization curling and flux closures in multiferroic tunnel junctions.

    abstract::Formation of domain walls in ferroelectrics is not energetically favourable in low-dimensional systems. Instead, vortex-type structures are formed that are driven by depolarization fields occurring in such systems. Consequently, polarization vortices have only been experimentally found in systems in which these fields...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13484

    authors: Peters JJP,Apachitei G,Beanland R,Alexe M,Sanchez AM

    更新日期:2016-11-16 00:00:00

  • Quantifying through-space charge transfer dynamics in π-coupled molecular systems.

    abstract::Understanding the role of intermolecular interaction on through-space charge transfer characteristics in π-stacked molecular systems is central to the rational design of electronic materials. However, a quantitative study of charge transfer in such systems is often difficult because of poor control over molecular morp...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2083

    authors: Batra A,Kladnik G,Vázquez H,Meisner JS,Floreano L,Nuckolls C,Cvetko D,Morgante A,Venkataraman L

    更新日期:2012-01-01 00:00:00

  • Asymmetric construction of tetrahedral chiral zinc with high configurational stability and catalytic activity.

    abstract::Chiral metal complexes show promise as asymmetric catalysts and optical materials. Chiral-at-metal complexes composed of achiral ligands have expanded the versatility and applicability of chiral metal complexes, especially for octahedral and half-sandwich complexes. However, Werner-type tetrahedral complexes with a st...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20074-7

    authors: Endo K,Liu Y,Ube H,Nagata K,Shionoya M

    更新日期:2020-12-09 00:00:00

  • Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea.

    abstract::Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. Due to its occasional side effects, reduction of caffeine in a natural way is of great importance and economic significance. Recent studies reveal that caffeine can be converted into non-stimulatory theacrine in the ra...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-15324-7

    authors: Zhang YH,Li YF,Wang Y,Tan L,Cao ZQ,Xie C,Xie G,Gong HB,Sun WY,Ouyang SH,Duan WJ,Lu X,Ding K,Kurihara H,Hu D,Zhang ZM,Abe I,He RR

    更新日期:2020-03-19 00:00:00

  • Thermal annihilation of photo-induced radicals following dynamic nuclear polarization to produce transportable frozen hyperpolarized 13C-substrates.

    abstract::Hyperpolarization via dynamic nuclear polarization (DNP) is pivotal for boosting magnetic resonance imaging (MRI) sensitivity and dissolution DNP can be used to perform in vivo real-time 13C MRI. The type of applications is however limited by the relatively fast decay time of the hyperpolarized spin state together wit...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15757

    authors: Capozzi A,Cheng T,Boero G,Roussel C,Comment A

    更新日期:2017-06-01 00:00:00

  • A framework to predict the price of energy for the end-users with applications to monetary and energy policies.

    abstract::Energy affects every single individual and entity in the world. Therefore, it is crucial to precisely quantify the "price of energy" and study how it evolves through time, through major political and social events, and through changes in energy and monetary policies. Here, we develop a predictive framework, an index t...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20203-2

    authors: Baratsas SG,Niziolek AM,Onel O,Matthews LR,Floudas CA,Hallermann DR,Sorescu SM,Pistikopoulos EN

    更新日期:2021-01-04 00:00:00

  • Systemic regulation of mammalian ageing and longevity by brain sirtuins.

    abstract::Sirtuins regulate numerous important biological processes in mammals, including various age-associated pathophysiologies. However, whether sirtuins are critical to control ageing and longevity in mammals has been controversial. Recent studies have demonstrated critical roles of sirtuins in the brain, especially the hy...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/ncomms5211

    authors: Satoh A,Imai S

    更新日期:2014-06-26 00:00:00

  • A general method for controlling and resolving rotational orientation of molecules in molecule-surface collisions.

    abstract::The outcome of molecule-surface collisions can be modified by pre-aligning the molecule; however, experiments accomplishing this are rare because of the difficulty of preparing molecules in aligned quantum states. Here we present a general solution to this problem based on magnetic manipulation of the rotational magne...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15357

    authors: Godsi O,Corem G,Alkoby Y,Cantin JT,Krems RV,Somers MF,Meyer J,Kroes GJ,Maniv T,Alexandrowicz G

    更新日期:2017-05-08 00:00:00

  • Atomically flat single-crystalline gold nanostructures for plasmonic nanocircuitry.

    abstract::Deep subwavelength integration of high-definition plasmonic nanostructures is of key importance in the development of future optical nanocircuitry for high-speed communication, quantum computation and lab-on-a-chip applications. To date, the experimental realization of proposed extended plasmonic networks consisting o...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1143

    authors: Huang JS,Callegari V,Geisler P,Brüning C,Kern J,Prangsma JC,Wu X,Feichtner T,Ziegler J,Weinmann P,Kamp M,Forchel A,Biagioni P,Sennhauser U,Hecht B

    更新日期:2010-01-01 00:00:00

  • A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.

    abstract::Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction s...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-18071-x

    authors: Piazza I,Beaton N,Bruderer R,Knobloch T,Barbisan C,Chandat L,Sudau A,Siepe I,Rinner O,de Souza N,Picotti P,Reiter L

    更新日期:2020-08-21 00:00:00

  • Motional Fock states for quantum-enhanced amplitude and phase measurements with trapped ions.

    abstract::The quantum noise of the vacuum limits the achievable sensitivity of quantum sensors. In non-classical measurement schemes the noise can be reduced to overcome this limitation. However, schemes based on squeezed or Schrödinger cat states require alignment of the relative phase between the measured interaction and the ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10576-4

    authors: Wolf F,Shi C,Heip JC,Gessner M,Pezzè L,Smerzi A,Schulte M,Hammerer K,Schmidt PO

    更新日期:2019-07-02 00:00:00

  • ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA.

    abstract::Mammals have nine different homologues (ALKBH1-9) of the Escherichia coli DNA repair demethylase AlkB. ALKBH2 is a genuine DNA repair enzyme, but the in vivo function of the other ALKBH proteins has remained elusive. It was recently shown that ALKBH8 contains an additional transfer RNA (tRNA) methyltransferase domain,...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1173

    authors: van den Born E,Vågbø CB,Songe-Møller L,Leihne V,Lien GF,Leszczynska G,Malkiewicz A,Krokan HE,Kirpekar F,Klungland A,Falnes PØ

    更新日期:2011-02-01 00:00:00

  • Laboratory measurements of resistivity in warm dense plasmas relevant to the microphysics of brown dwarfs.

    abstract::Since the observation of the first brown dwarf in 1995, numerous studies have led to a better understanding of the structures of these objects. Here we present a method for studying material resistivity in warm dense plasmas in the laboratory, which we relate to the microphysics of brown dwarfs through viscosity and e...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms9742

    authors: Booth N,Robinson AP,Hakel P,Clarke RJ,Dance RJ,Doria D,Gizzi LA,Gregori G,Koester P,Labate L,Levato T,Li B,Makita M,Mancini RC,Pasley J,Rajeev PP,Riley D,Wagenaars E,Waugh JN,Woolsey NC

    更新日期:2015-11-06 00:00:00

  • Room temperature magneto-optic effect in silicon light-emitting diodes.

    abstract::In weakly spin-orbit coupled materials, the spin-selective nature of recombination can give rise to large magnetic-field effects, e.g. on the electro-luminescence of molecular semiconductors. Although silicon has weak spin-orbit coupling, observing spin-dependent recombination through magneto-electroluminescence is ch...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-02804-6

    authors: Chiodi F,Bayliss SL,Barast L,Débarre D,Bouchiat H,Friend RH,Chepelianskii AD

    更新日期:2018-01-26 00:00:00

  • Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer.

    abstract::Pancreatic cancer is the fourth leading cause of cancer-related deaths in Japan. To identify risk loci, we perform a meta-analysis of three genome-wide association studies comprising 2,039 pancreatic cancer patients and 32,592 controls in the Japanese population. Here, we identify 3 (13q12.2, 13q22.1, and 16p12.3) gen...

    journal_title:Nature communications

    pub_type: 杂志文章,meta分析

    doi:10.1038/s41467-020-16711-w

    authors: Lin Y,Nakatochi M,Hosono Y,Ito H,Kamatani Y,Inoko A,Sakamoto H,Kinoshita F,Kobayashi Y,Ishii H,Ozaka M,Sasaki T,Matsuyama M,Sasahira N,Morimoto M,Kobayashi S,Fukushima T,Ueno M,Ohkawa S,Egawa N,Kuruma S,Mori M,

    更新日期:2020-06-24 00:00:00

  • Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.

    abstract::Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte activation and the DNA damage response. Cytoplasmic RNA granules are formed upon cell activation...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00454-2

    authors: Díaz-Muñoz MD,Kiselev VY,Le Novère N,Curk T,Ule J,Turner M

    更新日期:2017-09-13 00:00:00

  • Intensification of the meridional temperature gradient in the Great Barrier Reef following the Last Glacial Maximum.

    abstract::Tropical south-western Pacific temperatures are of vital importance to the Great Barrier Reef (GBR), but the role of sea surface temperatures (SSTs) in the growth of the GBR since the Last Glacial Maximum remains largely unknown. Here we present records of Sr/Ca and δ(18)O for Last Glacial Maximum and deglacial corals...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5102

    authors: Felis T,McGregor HV,Linsley BK,Tudhope AW,Gagan MK,Suzuki A,Inoue M,Thomas AL,Esat TM,Thompson WG,Tiwari M,Potts DC,Mudelsee M,Yokoyama Y,Webster JM

    更新日期:2014-06-17 00:00:00

  • Assembled molecular face-rotating polyhedra to transfer chirality from two to three dimensions.

    abstract::In nature, protein subunits on the capsids of many icosahedral viruses form rotational patterns, and mathematicians also incorporate asymmetric patterns into faces of polyhedra. Chemists have constructed molecular polyhedra with vacant or highly symmetric faces, but very little is known about constructing polyhedra wi...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms12469

    authors: Wang X,Wang Y,Yang H,Fang H,Chen R,Sun Y,Zheng N,Tan K,Lu X,Tian Z,Cao X

    更新日期:2016-08-24 00:00:00

  • MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL.

    abstract::The phosphorylation of eIF4E1 at serine 209 by MNK1 or MNK2 has been shown to initiate oncogenic mRNA translation, a process that favours cancer development and maintenance. Here, we interrogate the MNK-eIF4E axis in diffuse large B-cell lymphoma (DLBCL) and show a distinct distribution of MNK1 and MNK2 in germinal ce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6413

    authors: Landon AL,Muniandy PA,Shetty AC,Lehrmann E,Volpon L,Houng S,Zhang Y,Dai B,Peroutka R,Mazan-Mamczarz K,Steinhardt J,Mahurkar A,Becker KG,Borden KL,Gartenhaus RB

    更新日期:2014-11-18 00:00:00

  • Discovery of key whole-brain transitions and dynamics during human wakefulness and non-REM sleep.

    abstract::The modern understanding of sleep is based on the classification of sleep into stages defined by their electroencephalography (EEG) signatures, but the underlying brain dynamics remain unclear. Here we aimed to move significantly beyond the current state-of-the-art description of sleep, and in particular to characteri...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-08934-3

    authors: Stevner ABA,Vidaurre D,Cabral J,Rapuano K,Nielsen SFV,Tagliazucchi E,Laufs H,Vuust P,Deco G,Woolrich MW,Van Someren E,Kringelbach ML

    更新日期:2019-03-04 00:00:00

  • Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features.

    abstract::Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers....

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14229

    authors: Seki R,Li C,Fang Q,Hayashi S,Egawa S,Hu J,Xu L,Pan H,Kondo M,Sato T,Matsubara H,Kamiyama N,Kitajima K,Saito D,Liu Y,Gilbert MT,Zhou Q,Xu X,Shiroishi T,Irie N,Tamura K,Zhang G

    更新日期:2017-02-06 00:00:00

  • The transcript cleavage factor paralogue TFS4 is a potent RNA polymerase inhibitor.

    abstract::TFIIS-like transcript cleavage factors enhance the processivity and fidelity of archaeal and eukaryotic RNA polymerases. Sulfolobus solfataricus TFS1 functions as a bona fide cleavage factor, while the paralogous TFS4 evolved into a potent RNA polymerase inhibitor. TFS4 destabilises the TBP-TFB-RNAP pre-initiation com...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-02081-3

    authors: Fouqueau T,Blombach F,Hartman R,Cheung ACM,Young MJ,Werner F

    更新日期:2017-12-04 00:00:00

  • Andreev molecules in semiconductor nanowire double quantum dots.

    abstract::Chains of quantum dots coupled to superconductors are promising for the realization of the Kitaev model of a topological superconductor. While individual superconducting quantum dots have been explored, control of longer chains requires understanding of interdot coupling. Here, double quantum dots are defined by gate ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00665-7

    authors: Su Z,Tacla AB,Hocevar M,Car D,Plissard SR,Bakkers EPAM,Daley AJ,Pekker D,Frolov SM

    更新日期:2017-09-19 00:00:00

  • Enriched conditioning expands the regenerative ability of sensory neurons after spinal cord injury via neuronal intrinsic redox signaling.

    abstract::Overcoming the restricted axonal regenerative ability that limits functional repair following a central nervous system injury remains a challenge. Here we report a regenerative paradigm that we call enriched conditioning, which combines environmental enrichment (EE) followed by a conditioning sciatic nerve axotomy tha...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-20179-z

    authors: De Virgiliis F,Hutson TH,Palmisano I,Amachree S,Miao J,Zhou L,Todorova R,Thompson R,Danzi MC,Lemmon VP,Bixby JL,Wittig I,Shah AM,Di Giovanni S

    更新日期:2020-12-21 00:00:00

  • Selective and low temperature transition metal intercalation in layered tellurides.

    abstract::Layered materials embrace rich intercalation reactions to accommodate high concentrations of foreign species within their structures, and find many applications spanning from energy storage, ion exchange to secondary batteries. Light alkali metals are generally most easily intercalated due to their light mass, high ch...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms13809

    authors: Yajima T,Koshiko M,Zhang Y,Oguchi T,Yu W,Kato D,Kobayashi Y,Orikasa Y,Yamamoto T,Uchimoto Y,Green MA,Kageyama H

    更新日期:2016-12-14 00:00:00

  • Superplume mantle tracked isotopically the length of Africa from the Indian Ocean to the Red Sea.

    abstract::Seismological findings show a complex scenario of plume upwellings from a deep thermo-chemical anomaly (superplume) beneath the East African Rift System (EARS). It is unclear if these geophysical observations represent a true picture of the superplume and its influence on magmatism along the EARS. Thus, it is essentia...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13181-7

    authors: O'Connor JM,Jokat W,Regelous M,Kuiper KF,Miggins DP,Koppers AAP

    更新日期:2019-12-02 00:00:00

  • Epidemiology and biology of a herpesvirus in rabies endemic vampire bat populations.

    abstract::Rabies is a viral zoonosis transmitted by vampire bats across Latin America. Substantial public health and agricultural burdens remain, despite decades of bats culls and livestock vaccinations. Virally vectored vaccines that spread autonomously through bat populations are a theoretically appealing solution to managing...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-19832-4

    authors: Griffiths ME,Bergner LM,Broos A,Meza DK,Filipe ADS,Davison A,Tello C,Becker DJ,Streicker DG

    更新日期:2020-11-23 00:00:00

  • Universal mechanical exfoliation of large-area 2D crystals.

    abstract::Two-dimensional materials provide extraordinary opportunities for exploring phenomena arising in atomically thin crystals. Beginning with the first isolation of graphene, mechanical exfoliation has been a key to provide high-quality two-dimensional materials, but despite improvements it is still limited in yield, late...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-16266-w

    authors: Huang Y,Pan YH,Yang R,Bao LH,Meng L,Luo HL,Cai YQ,Liu GD,Zhao WJ,Zhou Z,Wu LM,Zhu ZL,Huang M,Liu LW,Liu L,Cheng P,Wu KH,Tian SB,Gu CZ,Shi YG,Guo YF,Cheng ZG,Hu JP,Zhao L,Yang GH,Sutter E,Sutter P,Wan

    更新日期:2020-05-15 00:00:00

  • In planta study of photosynthesis and photorespiration using NADPH and NADH/NAD+ fluorescent protein sensors.

    abstract::The challenge of monitoring in planta dynamic changes of NADP(H) and NAD(H) redox states at the subcellular level is considered a major obstacle in plant bioenergetics studies. Here, we introduced two circularly permuted yellow fluorescent protein sensors, iNAP and SoNar, into Arabidopsis thaliana to monitor the dynam...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-020-17056-0

    authors: Lim SL,Voon CP,Guan X,Yang Y,Gardeström P,Lim BL

    更新日期:2020-06-26 00:00:00