Protein-RNA networks revealed through covalent RNA marks.


: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 that adds uridines to the end of RNA. RNA targets bound by the chimeric protein in vivo are covalently marked with uridines and subsequently identified from extracted RNA via high-throughput sequencing. We used this approach to identify hundreds of RNAs bound by a Saccharomyces cerevisiae PUF protein, Puf3p. The results showed that although RNA-binding proteins productively bind specific RNAs to control their function, they also 'sample' RNAs without exerting a regulatory effect. We used the method to uncover hundreds of new and likely regulated targets for a protein without canonical RNA-binding domains, Bfr1p. RNA Tagging is well suited to detect and analyze protein-RNA networks in vivo.


Nat Methods


Nature methods


Lapointe CP,Wilinski D,Saunders HA,Wickens M




Has Abstract


2015-12-01 00:00:00














  • Fluorogenic DNA sequencing in PDMS microreactors.

    abstract::We developed a multiplex sequencing-by-synthesis method combining terminal phosphate-labeled fluorogenic nucleotides (TPLFNs) and resealable polydimethylsiloxane (PDMS) microreactors. In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent TPLFNs generates fluorophores, which are confin...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Sims PA,Greenleaf WJ,Duan H,Xie XS

    更新日期:2011-06-12 00:00:00

  • EPIC: software toolkit for elution profile-based inference of protein complexes.

    abstract::Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectromet...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Hu LZ,Goebels F,Tan JH,Wolf E,Kuzmanov U,Wan C,Phanse S,Xu C,Schertzberg M,Fraser AG,Bader GD,Emili A

    更新日期:2019-08-01 00:00:00

  • Doxycycline-dependent photoactivated gene expression in eukaryotic systems.

    abstract::High spatial and temporal resolution of conditional gene expression is typically difficult to achieve in whole tissues or organisms. We synthesized two reversibly inhibited, photoactivatable ('caged') doxycycline derivatives with different membrane permeabilities for precise spatial and temporal light-controlled activ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Cambridge SB,Geissler D,Calegari F,Anastassiadis K,Hasan MT,Stewart AF,Huttner WB,Hagen V,Bonhoeffer T

    更新日期:2009-07-01 00:00:00

  • Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry.

    abstract::Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Zuleta IA,Aranda-Díaz A,Li H,El-Samad H

    更新日期:2014-04-01 00:00:00

  • Microscopy. Self-healing light beams.

    abstract::The self-reconstructing properties of Bessel beams provide healing benefits in highly scattering media. ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Evanko D

    更新日期:2010-11-01 00:00:00

  • Finding S-sulfinylated proteins.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章


    authors: Doerr A

    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


    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

  • An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

    abstract::We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Corces MR,Trevino AE,Hamilton EG,Greenside PG,Sinnott-Armstrong NA,Vesuna S,Satpathy AT,Rubin AJ,Montine KS,Wu B,Kathiria A,Cho SW,Mumbach MR,Carter AC,Kasowski M,Orloff LA,Risca VI,Kundaje A,Khavari PA,Montine TJ,

    更新日期:2017-10-01 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


    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

  • A strategy for dissecting the architectures of native macromolecular assemblies.

    abstract::It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Shi Y,Pellarin R,Fridy PC,Fernandez-Martinez J,Thompson MK,Li Y,Wang QJ,Sali A,Rout MP,Chait BT

    更新日期:2015-12-01 00:00:00

  • Anna Moroni.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,新闻


    authors: Marx V

    更新日期:2018-11-01 00:00:00

  • Virtual microfluidics for digital quantification and single-cell sequencing.

    abstract::We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Xu L,Brito IL,Alm EJ,Blainey PC

    更新日期:2016-09-01 00:00:00

  • Measurement of mechanical tractions exerted by cells in three-dimensional matrices.

    abstract::Quantitative measurements of cell-generated forces have heretofore required that cells be cultured on two-dimensional substrates. We describe a technique to quantitatively measure three-dimensional traction forces exerted by cells fully encapsulated in well-defined elastic hydrogel matrices. Using this approach we mea...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Legant WR,Miller JS,Blakely BL,Cohen DM,Genin GM,Chen CS

    更新日期:2010-12-01 00:00:00

  • Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy.

    abstract::Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Keller PJ,Schmidt AD,Santella A,Khairy K,Bao Z,Wittbrodt J,Stelzer EH

    更新日期:2010-08-01 00:00:00

  • Single-cell genomics.

    abstract::Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kalisky T,Quake SR

    更新日期:2011-04-01 00:00:00

  • Genetic incorporation of unnatural amino acids into proteins in mammalian cells.

    abstract::We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Liu W,Brock A,Chen S,Chen S,Schultz PG

    更新日期:2007-03-01 00:00:00

  • Channelrhodopsin-2 and optical control of excitable cells.

    abstract::Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrho...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Zhang F,Wang LP,Boyden ES,Deisseroth K

    更新日期:2006-10-01 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


    authors: Doerr A

    更新日期:2010-09-01 00:00:00

  • Varying label density allows artifact-free analysis of membrane-protein nanoclusters.

    abstract::We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quant...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Baumgart F,Arnold AM,Leskovar K,Staszek K,Fölser M,Weghuber J,Stockinger H,Schütz GJ

    更新日期:2016-08-01 00:00:00

  • Tracking transmitter-gated P2X cation channel activation in vitro and in vivo.

    abstract::We present a noninvasive approach to track activation of ATP-gated P2X receptors and potentially other transmitter-gated cation channels that show calcium fluxes. We genetically engineered rat P2X receptors to carry calcium sensors near the channel pore and tested this as a reporter for P2X(2) receptor opening. The me...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Richler E,Chaumont S,Shigetomi E,Sagasti A,Khakh BS

    更新日期:2008-01-01 00:00:00

  • Efficient and quantitative high-throughput tRNA sequencing.

    abstract::Despite its biological importance, tRNA has not been adequately sequenced by standard methods because of its abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. We achieved efficient and quantitative tRNA sequencing in HEK293T cells by using engineered demethylases to...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Zheng G,Qin Y,Clark WC,Dai Q,Yi C,He C,Lambowitz AM,Pan T

    更新日期:2015-09-01 00:00:00

  • Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution.

    abstract::We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Kompauer M,Heiles S,Spengler B

    更新日期:2017-01-01 00:00:00

  • A Cre-inducible diphtheria toxin receptor mediates cell lineage ablation after toxin administration.

    abstract::A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Buch T,Heppner FL,Tertilt C,Heinen TJ,Kremer M,Wunderlich FT,Jung S,Waisman A

    更新日期:2005-06-01 00:00:00

  • Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies.

    abstract::The ability to selectively interfere with post-translationally modified proteins would have many biological and therapeutic applications. However, post-translational modifications cannot be selectively targeted by nucleic-acid-based interference approaches. Here we describe post-translational intracellular silencing a...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Chirichella M,Lisi S,Fantini M,Goracci M,Calvello M,Brandi R,Arisi I,D'Onofrio M,Di Primio C,Cattaneo A

    更新日期:2017-03-01 00:00:00

  • CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

    abstract::Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( ...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Lever J,Zhao EY,Grewal J,Jones MR,Jones SJM

    更新日期:2019-06-01 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


    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

  • Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

    abstract::The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Dai Q,Moshitch-Moshkovitz S,Han D,Kol N,Amariglio N,Rechavi G,Dominissini D,He C

    更新日期:2017-07-01 00:00:00

  • 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 ...

    journal_title:Nature methods

    pub_type: 杂志文章


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

    更新日期:2011-02-01 00:00:00

  • Efficient incorporation of unnatural amino acids into proteins in Escherichia coli.

    abstract::We have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tR...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Ryu Y,Schultz PG

    更新日期:2006-04-01 00:00:00

  • Proteomic and phosphoproteomic comparison of human ES and iPS cells.

    abstract::Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very larg...

    journal_title:Nature methods

    pub_type: 杂志文章


    authors: Phanstiel DH,Brumbaugh J,Wenger CD,Tian S,Probasco MD,Bailey DJ,Swaney DL,Tervo MA,Bolin JM,Ruotti V,Stewart R,Thomson JA,Coon JJ

    更新日期:2011-09-11 00:00:00