当前位置： SCI文献检索 > Nature Communications期刊下所有文献 > A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions.

A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions.

Abstract：

:Clustered regularly-interspaced palindromic repeats (CRISPR)-based genetic screens using single-guide-RNA (sgRNA) libraries have proven powerful to identify genetic regulators. Applying CRISPR screens to interrogate functional elements in noncoding regions requires generating sgRNA libraries that are densely covering, and ideally inexpensive, easy to implement and flexible for customization. Here we present a Molecular Chipper technology for generating dense sgRNA libraries for genomic regions of interest, and a proof-of-principle screen that identifies novel cis-regulatory domains for miR-142 biogenesis. The Molecular Chipper approach utilizes a combination of random fragmentation and a type III restriction enzyme to derive a densely covering sgRNA library from input DNA. Applying this approach to 17 microRNAs and their flanking regions and with a reporter for miR-142 activity, we identify both the pre-miR-142 region and two previously unrecognized cis-domains important for miR-142 biogenesis, with the latter regulating miR-142 processing. This strategy will be useful for identifying functional noncoding elements in mammalian genomes.

journal_name

Nat Commun

journal_title

Nature communications

authors

Cheng J,Roden CA,Pan W,Zhu S,Baccei A,Pan X,Jiang T,Kluger Y,Weissman SM,Guo S,Flavell RA,Ding Y,Lu J

doi

10.1038/ncomms11178

subject

Has Abstract

pub_date

2016-03-30 00:00:00

pages

11178

issn

2041-1723

pii

ncomms11178

journal_volume

7

pub_type

杂志文章

相关文献

Nature Communications文献大全
  • Slower carriers limit charge generation in organic semiconductor light-harvesting systems.

    abstract：:Blends of electron-donating and -accepting organic semiconductors are widely used as photoactive materials in next-generation solar cells and photodetectors. The yield of free charges in these systems is often determined by the separation of interfacial electron-hole pairs, which is expected to depend on the ability o...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms11944

    authors： Stolterfoht M,Armin A,Shoaee S,Kassal I,Burn P,Meredith P

    更新日期：2016-06-21 00:00:00

  • Exceptionally well-preserved Cretaceous microfossils reveal new biomineralization styles.

    abstract：:Calcareous microplankton shells form the dominant components of ancient and modern pelagic sea-floor carbonates and are widely used in palaeoenvironmental reconstructions. The efficacy of these applications, however, is dependent upon minimal geochemical alteration during diagenesis, but these modifying processes are ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3052

    authors： Wendler JE,Bown P

    更新日期：2013-01-01 00:00:00

  • A transposable element insertion is associated with an alternative life history strategy.

    abstract：:Tradeoffs affect resource allocation during development and result in fitness consequences that drive the evolution of life history strategies. Yet despite their importance, we know little about the mechanisms underlying life history tradeoffs. Many species of Colias butterflies exhibit an alternative life history str...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-13596-2

    authors： Woronik A,Tunström K,Perry MW,Neethiraj R,Stefanescu C,Celorio-Mancera MP,Brattström O,Hill J,Lehmann P,Käkelä R,Wheat CW

    更新日期：2019-12-17 00:00:00

  • The atypical chemokine receptor 3 interacts with Connexin 43 inhibiting astrocytic gap junctional intercellular communication.

    abstract：:The atypical chemokine receptor 3 (ACKR3) plays a pivotal role in directing the migration of various cellular populations and its over-expression in tumors promotes cell proliferation and invasiveness. The intracellular signaling pathways transducing ACKR3-dependent effects remain poorly characterized, an issue we add...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-18634-y

    authors： Fumagalli A,Heuninck J,Pizzoccaro A,Moutin E,Koenen J,Séveno M,Durroux T,Junier MP,Schlecht-Louf G,Bachelerie F,Schütz D,Stumm R,Smit MJ,Guérineau NC,Chaumont-Dubel S,Marin P

    更新日期：2020-09-25 00:00:00

  • Targeting VEGF-A in myeloid cells enhances natural killer cell responses to chemotherapy and ameliorates cachexia.

    abstract：:Chemotherapy remains a mainstay of cancer treatment but its use is often limited by the development of adverse reactions. Severe loss of body weight (cachexia) is a frequent cause of death in cancer patients and is exacerbated by chemotherapy. We show that genetic inactivation of vascular endothelial growth factor (VE...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12528

    authors： Klose R,Krzywinska E,Castells M,Gotthardt D,Putz EM,Kantari-Mimoun C,Chikdene N,Meinecke AK,Schrödter K,Helfrich I,Fandrey J,Sexl V,Stockmann C

    更新日期：2016-08-19 00:00:00

  • Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids.

    abstract：:C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-20035-0

    authors： Pfeiffer M,Nidetzky B

    更新日期：2020-12-08 00:00:00

  • Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR.

    abstract：:Epistasis emerges when the effects of an amino acid depend on the identities of interacting residues. This phenomenon shapes fitness landscapes, which have the power to reveal evolutionary paths and inform evolution of desired functions. However, there is a need for easily implemented, high-throughput methods to captu...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-14495-7

    authors： Yoo JI,Daugherty PS,O'Malley MA

    更新日期：2020-02-04 00:00:00

  • Exploring the wavefront of hard X-ray free-electron laser radiation.

    abstract：:The high photon flux and femtosecond pulse duration of hard X-ray free-electron lasers have spurred a large variety of novel and fascinating experiments in physical, chemical and biological sciences. Many of these experiments depend fundamentally on a clean, well-defined wavefront. Here we explore the wavefront proper...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms1950

    authors： Rutishauser S,Samoylova L,Krzywinski J,Bunk O,Grünert J,Sinn H,Cammarata M,Fritz DM,David C

    更新日期：2012-07-10 00:00:00

  • Plant macrofossil evidence for an early onset of the Holocene summer thermal maximum in northernmost Europe.

    abstract：:Holocene summer temperature reconstructions from northern Europe based on sedimentary pollen records suggest an onset of peak summer warmth around 9,000 years ago. However, pollen-based temperature reconstructions are largely driven by changes in the proportions of tree taxa, and thus the early-Holocene warming signal...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms7809

    authors： Väliranta M,Salonen JS,Heikkilä M,Amon L,Helmens K,Klimaschewski A,Kuhry P,Kultti S,Poska A,Shala S,Veski S,Birks HH

    更新日期：2015-04-10 00:00:00

  • Archimedes' law explains penetration of solids into granular media.

    abstract：:Understanding the response of granular matter to intrusion of solid objects is key to modelling many aspects of behaviour of granular matter, including plastic flow. Here we report a general model for such a quasistatic process. Using a range of experiments, we first show that the relation between the penetration dept...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03344-3

    authors： Kang W,Feng Y,Liu C,Blumenfeld R

    更新日期：2018-03-16 00:00:00

  • Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera.

    abstract：:Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar s...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-18739-4

    authors： Song H,Béthoux O,Shin S,Donath A,Letsch H,Liu S,McKenna DD,Meng G,Misof B,Podsiadlowski L,Zhou X,Wipfler B,Simon S

    更新日期：2020-10-02 00:00:00

  • Engineering skyrmions in transition-metal multilayers for spintronics.

    abstract：:Magnetic skyrmions are localized, topologically protected spin structures that have been proposed for storing or processing information due to their intriguing dynamical and transport properties. Important in terms of applications is the recent discovery of interface stabilized skyrmions as evidenced in ultra-thin tra...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms11779

    authors： Dupé B,Bihlmayer G,Böttcher M,Blügel S,Heinze S

    更新日期：2016-06-03 00:00:00

  • Uranium transport in acidic brines under reducing conditions.

    abstract：:The behavior of uranium in environments, ranging from those of natural systems responsible for the formation of uranium deposits to those of nuclear reactors providing 11% of the world's electricity, is governed by processes involving high-temperature aqueous solutions. It has been well documented that uranium is mobi...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03564-7

    authors： Timofeev A,Migdisov AA,Williams-Jones AE,Roback R,Nelson AT,Xu H

    更新日期：2018-04-16 00:00:00

  • Author Correction: Band gap closure, incommensurability and molecular dissociation of dense chlorine.

    abstract：:The original version of this Article omitted references to previous experimental reports on solid hydrogen that are relevant for a full understanding of the context of the previous work. The added references are: 47. Akahama, Y. et al. Evidence from x-ray diffraction of orientational ordering in phase III of solid hyd...

    journal_title：Nature communications

    pub_type： 已发布勘误

    doi：10.1038/s41467-019-10187-z

    authors： Dalladay-Simpson P,Binns J,Peña-Alvarez M,Donnelly ME,Greenberg E,Prakapenka V,Chen XJ,Gregoryanz E,Howie RT

    更新日期：2019-05-03 00:00:00

  • Observation of a new superfluid phase for 3He embedded in nematically ordered aerogel.

    abstract：:In bulk superfluid 3He at zero magnetic field, two phases emerge with the B-phase stable everywhere except at high pressures and temperatures, where the A-phase is favoured. Aerogels with nanostructure smaller than the superfluid coherence length are the only means to introduce disorder into the superfluid. Here we us...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms12975

    authors： Zhelev N,Reichl M,Abhilash TS,Smith EN,Nguyen KX,Mueller EJ,Parpia JM

    更新日期：2016-09-27 00:00:00

  • Region-specific and state-dependent action of striatal GABAergic interneurons.

    abstract：:Striatum processes a wide range of functions including goal-directed behavior and habit formation, respectively encoded by the dorsomedial striatum (DMS) and dorsolateral striatum (DLS). GABAergic feedforward inhibition is known to control the integration of cortical information by striatal projection neurons (SPNs). ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-05847-5

    authors： Fino E,Vandecasteele M,Perez S,Saudou F,Venance L

    更新日期：2018-08-21 00:00:00

  • Author Correction: Mutant p53 drives clonal hematopoiesis through modulating epigenetic pathway.

    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/s41467-020-17555-0

    authors： Chen S,Wang Q,Yu H,Capitano ML,Vemula S,Nabinger SC,Gao R,Yao C,Kobayashi M,Geng Z,Fahey A,Henley D,Liu SZ,Barajas S,Cai W,Wolf ER,Ramdas B,Cai Z,Gao H,Luo N,Sun Y,Wong TN,Link DC,Liu Y,Boswell HS,Mayo L

    更新日期：2020-07-28 00:00:00

  • Casimir forces on a silicon micromechanical chip.

    abstract：:Quantum fluctuations give rise to van der Waals and Casimir forces that dominate the interaction between electrically neutral objects at sub-micron separations. Under the trend of miniaturization, such quantum electrodynamical effects are expected to play an important role in micro- and nano-mechanical devices. Nevert...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms2842

    authors： Zou J,Marcet Z,Rodriguez AW,Reid MT,McCauley AP,Kravchenko II,Lu T,Bao Y,Johnson SG,Chan HB

    更新日期：2013-01-01 00:00:00

  • Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions.

    abstract：:OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-10966-8

    authors： Birtley JR,Alomary M,Zanini E,Antony J,Maben Z,Weaver GC,Von Arx C,Mura M,Marinho AT,Lu H,Morecroft EVN,Karali E,Chayen NE,Tate EW,Jurewicz M,Stern LJ,Recchi C,Gabra H

    更新日期：2019-07-17 00:00:00

  • Cell-permeable organic fluorescent probes for live-cell long-term super-resolution imaging reveal lysosome-mitochondrion interactions.

    abstract：:Characterizing the long-term nanometer-scale interactions between lysosomes and mitochondria in live cells is essential for understanding their functions but remains challenging due to limitations of the existing fluorescent probes. Here, we develop cell-permeable organic fluorescent probes for lysosomes with excellen...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-01503-6

    authors： Han Y,Li M,Qiu F,Zhang M,Zhang YH

    更新日期：2017-11-03 00:00:00

  • Evolution and structure of clinically relevant gene fusions in multiple myeloma.

    abstract：:Multiple myeloma is a plasma cell blood cancer with frequent chromosomal translocations leading to gene fusions. To determine the clinical relevance of fusion events, we detect gene fusions from a cohort of 742 patients from the Multiple Myeloma Research Foundation CoMMpass Study. Patients with multiple clinic visits ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-16434-y

    authors： Foltz SM,Gao Q,Yoon CJ,Sun H,Yao L,Li Y,Jayasinghe RG,Cao S,King J,Kohnen DR,Fiala MA,Ding L,Vij R

    更新日期：2020-05-29 00:00:00

  • Merging of metal nanoparticles driven by selective wettability of silver nanostructures.

    abstract：:The welding and sintering of nanomaterials is relevant, for example, to form electrical contacts between metallic particles in printed electronic devices. Usually the welding of nanoparticles is achieved at high temperatures. Here we find that merging of two different metals, silver and gold nanoparticles, occurs on c...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms3994

    authors： Grouchko M,Roitman P,Zhu X,Popov I,Kamyshny A,Su H,Magdassi S

    更新日期：2014-01-01 00:00:00

  • Microbial carbon use efficiency predicted from genome-scale metabolic models.

    abstract：:Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-11488-z

    authors： Saifuddin M,Bhatnagar JM,Segrè D,Finzi AC

    更新日期：2019-08-08 00:00:00

  • Task complexity interacts with state-space uncertainty in the arbitration between model-based and model-free learning.

    abstract：:It has previously been shown that the relative reliability of model-based and model-free reinforcement-learning (RL) systems plays a role in the allocation of behavioral control between them. However, the role of task complexity in the arbitration between these two strategies remains largely unknown. Here, using a com...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-019-13632-1

    authors： Kim D,Park GY,O Doherty JP,Lee SW

    更新日期：2019-12-16 00:00:00

  • Stromal PTEN determines mammary epithelial response to radiotherapy.

    abstract：:The importance of the tumor-associated stroma in cancer progression is clear. However, it remains uncertain whether early events in the stroma are capable of initiating breast tumorigenesis. Here, we show that in the mammary glands of non-tumor bearing mice, stromal-specific phosphatase and tensin homolog (Pten) delet...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-05266-6

    authors： Sizemore GM,Balakrishnan S,Thies KA,Hammer AM,Sizemore ST,Trimboli AJ,Cuitiño MC,Steck SA,Tozbikian G,Kladney RD,Shinde N,Das M,Park D,Majumder S,Krishnan S,Yu L,Fernandez SA,Chakravarti A,Shields PG,White JR,Yee

    更新日期：2018-07-17 00:00:00

  • Plasmapause surface wave oscillates the magnetosphere and diffuse aurora.

    abstract：:Energy circulation in geospace lies at the heart of space weather research. In the inner magnetosphere, the steep plasmapause boundary separates the cold dense plasmasphere, which corotates with the planet, from the hot ring current/plasma sheet outside. Theoretical studies suggested that plasmapause surface waves rel...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-020-15506-3

    authors： He F,Guo RL,Dunn WR,Yao ZH,Zhang HS,Hao YX,Shi QQ,Rong ZJ,Liu J,Tian AM,Zhang XX,Wei Y,Zhang YL,Zong QG,Pu ZY,Wan WX

    更新日期：2020-04-03 00:00:00

  • Ionic liquid gating control of RKKY interaction in FeCoB/Ru/FeCoB and (Pt/Co)2/Ru/(Co/Pt)2 multilayers.

    abstract：:To overcome the fundamental challenge of the weak natural response of antiferromagnetic materials under a magnetic field, voltage manipulation of antiferromagnetic interaction is developed to realize ultrafast, high-density, and power efficient antiferromagnetic spintronics. Here, we report a low voltage modulation of...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-018-03356-z

    authors： Yang Q,Wang L,Zhou Z,Wang L,Zhang Y,Zhao S,Dong G,Cheng Y,Min T,Hu Z,Chen W,Xia K,Liu M

    更新日期：2018-03-07 00:00:00

  • Membrane curvature induced by proximity of anionic phospholipids can initiate endocytosis.

    abstract：:The plasma membrane is uniquely enriched in phosphatidylserine (PtdSer). This anionic phospholipid is restricted almost exclusively to the inner leaflet of the plasmalemma. Because of their high density, the headgroups of anionic lipids experience electrostatic repulsion that, being exerted asymmetrically, is predicte...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/s41467-017-01554-9

    authors： Hirama T,Lu SM,Kay JG,Maekawa M,Kozlov MM,Grinstein S,Fairn GD

    更新日期：2017-11-09 00:00:00

  • The insulin and IGF1 receptor kinase domains are functional dimers in the activated state.

    abstract：:The insulin receptor (IR) and insulin-like growth factor-1 receptor (IGF1R) are highly related receptor tyrosine kinases with a disulfide-linked homodimeric architecture. Ligand binding to the receptor ectodomain triggers tyrosine autophosphorylation of the cytoplasmic domains, which stimulates catalytic activity and ...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms7406

    authors： Cabail MZ,Li S,Lemmon E,Bowen ME,Hubbard SR,Miller WT

    更新日期：2015-03-11 00:00:00

  • Breather soliton dynamics in microresonators.

    abstract：:The generation of temporal cavity solitons in microresonators results in coherent low-noise optical frequency combs that are critical for applications in spectroscopy, astronomy, navigation or telecommunications. Breather solitons also form an important part of many different classes of nonlinear wave systems, manifes...

    journal_title：Nature communications

    pub_type： 杂志文章

    doi：10.1038/ncomms14569

    authors： Yu M,Jang JK,Okawachi Y,Griffith AG,Luke K,Miller SA,Ji X,Lipson M,Gaeta AL

    更新日期：2017-02-24 00:00:00