A transgenic mouse for in vivo detection of endogenous labeled mRNA.

Abstract:

:Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse line with an MS2 binding site (MBS) cassette targeted to the 3' untranslated region of the essential β-actin gene. As β-actin-MBS was ubiquitously expressed, we could uniquely address endogenous mRNA regulation in any tissue or cell type. We simultaneously followed transcription from the β-actin alleles in real time and observed transcriptional bursting in response to serum stimulation with precise temporal resolution. We tracked single endogenous labeled mRNA particles being transported in primary hippocampal neurons. The MBS cassette also enabled high-sensitivity fluorescence in situ hybridization (FISH), allowing detection and localization of single β-actin mRNA molecules in various mouse tissues.

journal_name

Nat Methods

journal_title

Nature methods

authors

Lionnet T,Czaplinski K,Darzacq X,Shav-Tal Y,Wells AL,Chao JA,Park HY,de Turris V,Lopez-Jones M,Singer RH

doi

10.1038/nmeth.1551

subject

Has Abstract

pub_date

2011-02-01 00:00:00

pages

165-70

issue

2

eissn

1548-7091

issn

1548-7105

pii

nmeth.1551

journal_volume

8

pub_type

杂志文章
  • High-efficiency labeling of sialylated glycoproteins on living cells.

    abstract::We describe a simple method for efficiently labeling cell-surface sialic acid-containing glycans on living animal cells. The method uses mild periodate oxidation to generate an aldehyde on sialic acids, followed by aniline-catalyzed oxime ligation with a suitable tag. Aniline catalysis dramatically accelerates oxime l...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1305

    authors: Zeng Y,Ramya TN,Dirksen A,Dawson PE,Paulson JC

    更新日期:2009-03-01 00:00:00

  • CLARITY for mapping the nervous system.

    abstract::With potential relevance for brain-mapping work, hydrogel-based structures can now be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue. This process creates a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2481

    authors: Chung K,Deisseroth K

    更新日期:2013-06-01 00:00:00

  • Cell-type specific sequencing of microRNAs from complex animal tissues.

    abstract::MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4610

    authors: Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

    更新日期:2018-04-01 00:00:00

  • The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells.

    abstract::Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, terme...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2895

    authors: Petschnigg J,Groisman B,Kotlyar M,Taipale M,Zheng Y,Kurat CF,Sayad A,Sierra JR,Mattiazzi Usaj M,Snider J,Nachman A,Krykbaeva I,Tsao MS,Moffat J,Pawson T,Lindquist S,Jurisica I,Stagljar I

    更新日期:2014-05-01 00:00:00

  • Author Correction: Genetically engineered cerebral organoids model brain tumor formation.

    abstract::In the originally published paper, the "before" image for the afatinib condition in Fig. 6c was incorrect. Instead of an image displaying a GBM-3 neoplastic organoid before afatinib treatment, this panel showed an image from the GBM-2 control (DMSO) group before treatment. This error has now been corrected in the HTML...

    journal_title:Nature methods

    pub_type: 已发布勘误

    doi:10.1038/s41592-018-0118-8

    authors: Bian S,Repic M,Guo Z,Kavirayani A,Burkard T,Bagley JA,Krauditsch C,Knoblich JA

    更新日期:2018-09-01 00:00:00

  • PyClone: statistical inference of clonal population structure in cancer.

    abstract::We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2883

    authors: Roth A,Khattra J,Yap D,Wan A,Laks E,Biele J,Ha G,Aparicio S,Bouchard-Côté A,Shah SP

    更新日期:2014-04-01 00:00:00

  • An active texture-based digital atlas enables automated mapping of structures and markers across brains.

    abstract::Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to defi...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0328-8

    authors: Chen Y,McElvain LE,Tolpygo AS,Ferrante D,Friedman B,Mitra PP,Karten HJ,Freund Y,Kleinfeld D

    更新日期:2019-04-01 00:00:00

  • Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy.

    abstract::We discuss unique features of lens-free computational imaging tools and report some of their emerging results for wide-field on-chip microscopy, such as the achievement of a numerical aperture (NA) of ∼0.8-0.9 across a field of view (FOV) of more than 20 mm(2) or an NA of ∼0.1 across a FOV of ∼18 cm(2), which correspo...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2114

    authors: Greenbaum A,Luo W,Su TW,Göröcs Z,Xue L,Isikman SO,Coskun AF,Mudanyali O,Ozcan A

    更新日期:2012-09-01 00:00:00

  • Unified rational protein engineering with sequence-based deep representation learning.

    abstract::Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0598-1

    authors: Alley EC,Khimulya G,Biswas S,AlQuraishi M,Church GM

    更新日期:2019-12-01 00:00:00

  • Tracking protein aggregation and mislocalization in cells with flow cytometry.

    abstract::We applied pulse-shape analysis (PulSA) to monitor protein localization changes in mammalian cells by flow cytometry. PulSA enabled high-throughput tracking of protein aggregation, translocation from the cytoplasm to the nucleus and trafficking from the plasma membrane to the Golgi as well as stress-granule formation....

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1930

    authors: Ramdzan YM,Polling S,Chia CP,Ng IH,Ormsby AR,Croft NP,Purcell AW,Bogoyevitch MA,Ng DC,Gleeson PA,Hatters DM

    更新日期:2012-03-18 00:00:00

  • Mapping of signaling networks through synthetic genetic interaction analysis by RNAi.

    abstract::The analysis of synthetic genetic interaction networks can reveal how biological systems achieve a high level of complexity with a limited repertoire of components. Studies in yeast and bacteria have taken advantage of collections of deletion strains to construct matrices of quantitative interaction profiles and infer...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1581

    authors: Horn T,Sandmann T,Fischer B,Axelsson E,Huber W,Boutros M

    更新日期:2011-04-01 00:00:00

  • Molecular engineering: Unnatural design.

    abstract::Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/nmeth0910-671

    authors: Doerr A

    更新日期:2010-09-01 00:00:00

  • DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

    abstract::As a result of recent improvements in mass spectrometry (MS), there is increased interest in data-independent acquisition (DIA) strategies in which all peptides are systematically fragmented using wide mass-isolation windows ('multiplex fragmentation'). DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive c...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3255

    authors: Tsou CC,Avtonomov D,Larsen B,Tucholska M,Choi H,Gingras AC,Nesvizhskii AI

    更新日期:2015-03-01 00:00:00

  • Protein-RNA networks revealed through covalent RNA marks.

    abstract::Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3651

    authors: Lapointe CP,Wilinski D,Saunders HA,Wickens M

    更新日期:2015-12-01 00:00:00

  • Directed evolution of APEX2 for electron microscopy and proximity labeling.

    abstract::APEX is an engineered peroxidase that functions as an electron microscopy tag and a promiscuous labeling enzyme for live-cell proteomics. Because limited sensitivity precludes applications requiring low APEX expression, we used yeast-display evolution to improve its catalytic efficiency. APEX2 is far more active in ce...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3179

    authors: Lam SS,Martell JD,Kamer KJ,Deerinck TJ,Ellisman MH,Mootha VK,Ting AY

    更新日期:2015-01-01 00:00:00

  • Onco-proteogenomics: cancer proteomics joins forces with genomics.

    abstract::The complexities of tumor genomes are rapidly being uncovered, but how they are regulated into functional proteomes remains poorly understood. Standard proteomics workflows use databases of known proteins, but these databases do not capture the uniqueness of the cancer transcriptome, with its point mutations, unusual ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3138

    authors: Alfaro JA,Sinha A,Kislinger T,Boutros PC

    更新日期:2014-11-01 00:00:00

  • Detection of minor drug-resistant populations by parallel allele-specific sequencing.

    abstract::We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we s...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth995

    authors: Cai F,Chen H,Hicks CB,Bartlett JA,Zhu J,Gao F

    更新日期:2007-02-01 00:00:00

  • FRETting for a more detailed interactome.

    abstract::A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0207-112b

    authors: Kaganman I

    更新日期:2007-02-01 00:00:00

  • Analysis of the Human Protein Atlas Image Classification competition.

    abstract::Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and pr...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0658-6

    authors: Ouyang W,Winsnes CF,Hjelmare M,Cesnik AJ,Åkesson L,Xu H,Sullivan DP,Dai S,Lan J,Jinmo P,Galib SM,Henkel C,Hwang K,Poplavskiy D,Tunguz B,Wolfinger RD,Gu Y,Li C,Xie J,Buslov D,Fironov S,Kiselev A,Panchenko D,C

    更新日期:2019-12-01 00:00:00

  • Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

    abstract::The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and b...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3407

    authors: Ewing AD,Houlahan KE,Hu Y,Ellrott K,Caloian C,Yamaguchi TN,Bare JC,P'ng C,Waggott D,Sabelnykova VY,ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants.,Kellen MR,Norman TC,Haussler D,Friend SH,Stolovitzky G,Ma

    更新日期:2015-07-01 00:00:00

  • Bending the genome.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0270-1

    authors: Rusk N

    更新日期:2019-01-01 00:00:00

  • A general design strategy for protein-responsive riboswitches in mammalian cells.

    abstract::RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozyme...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3136

    authors: Ausländer S,Stücheli P,Rehm C,Ausländer D,Hartig JS,Fussenegger M

    更新日期:2014-11-01 00:00:00

  • On the art of identifying effective and specific siRNAs.

    abstract::Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth911

    authors: Pei Y,Tuschl T

    更新日期:2006-09-01 00:00:00

  • Conformal nanopatterning of extracellular matrix proteins onto topographically complex surfaces.

    abstract::Our Patterning on Topography (PoT) printing technique enables fibronectin, laminin and other proteins to be applied to biomaterial surfaces in complex geometries that are inaccessible using traditional soft lithography techniques. Engineering combinatorial surfaces that integrate topographical and biochemical micropat...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3210

    authors: Sun Y,Jallerat Q,Szymanski JM,Feinberg AW

    更新日期:2015-02-01 00:00:00

  • Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures.

    abstract::Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1539

    authors: Doyon Y,Vo TD,Mendel MC,Greenberg SG,Wang J,Xia DF,Miller JC,Urnov FD,Gregory PD,Holmes MC

    更新日期:2011-01-01 00:00:00

  • Anna Moroni.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,新闻

    doi:10.1038/s41592-018-0192-y

    authors: Marx V

    更新日期:2018-11-01 00:00:00

  • Imaging cellular ultrastructures using expansion microscopy (U-ExM).

    abstract::Determining the structure and composition of macromolecular assemblies is a major challenge in biology. Here we describe ultrastructure expansion microscopy (U-ExM), an extension of expansion microscopy that allows the visualization of preserved ultrastructures by optical microscopy. This method allows for near-native...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0238-1

    authors: Gambarotto D,Zwettler FU,Le Guennec M,Schmidt-Cernohorska M,Fortun D,Borgers S,Heine J,Schloetel JG,Reuss M,Unser M,Boyden ES,Sauer M,Hamel V,Guichard P

    更新日期:2019-01-01 00:00:00

  • Comparing the performance of biomedical clustering methods.

    abstract::Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein d...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3583

    authors: Wiwie C,Baumbach J,Röttger R

    更新日期:2015-11-01 00:00:00

  • Mass spectrometry-based functional proteomics: from molecular machines to protein networks.

    abstract::The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignmen...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth1093

    authors: Köcher T,Superti-Furga G

    更新日期:2007-10-01 00:00:00

  • Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering.

    abstract::We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1255

    authors: Cammarata M,Levantino M,Schotte F,Anfinrud PA,Ewald F,Choi J,Cupane A,Wulff M,Ihee H

    更新日期:2008-10-01 00:00:00