当前位置： SCI文献检索 > NATURE STRUCTURAL & MOLECULAR BIOLOGY期刊下所有文献 > Quantification of translation uncovers the functions of the alternative transcriptome.

Quantification of translation uncovers the functions of the alternative transcriptome.

Abstract：

:Translation has a fundamental function in defining the fate of the transcribed genome. RNA-sequencing (RNA-seq) data enable the quantification of complex transcript mixtures, often detecting several transcript isoforms of unknown functions for one gene. Here, we describe ORFquant, a method to annotate and quantify translation at the level of single open reading frames (ORFs), using information from Ribo-seq data. By developing an approach for transcript filtering, we quantify translation transcriptome-wide, revealing translated ORFs on multiple isoforms per gene. For most genes, one ORF represents the dominant translation product, but we also detect genes with translated ORFs on multiple transcript isoforms, including targets of RNA surveillance mechanisms. Measuring translation across human cell lines reveals the extent of gene-specific differences in protein production, supported by steady-state protein abundance estimates. Computational analysis of Ribo-seq data with ORFquant (https://github.com/lcalviell/ORFquant) provides insights into the heterogeneous functions of complex transcriptomes.

journal_name

Nat Struct Mol Biol

journal_title

Nature structural & molecular biology

authors

Calviello L,Hirsekorn A,Ohler U

doi

10.1038/s41594-020-0450-4

subject

Has Abstract

pub_date

2020-08-01 00:00:00

pages

717-725

issue

8

eissn

1545-9993

issn

1545-9985

pii

10.1038/s41594-020-0450-4

journal_volume

27

pub_type

杂志文章

相关文献

NATURE STRUCTURAL & MOLECULAR BIOLOGY文献大全
  • Multiple functions of MRN in end-joining pathways during isotype class switching.

    abstract：:The Mre11-Rad50-NBS1 (MRN) complex has many roles in response to DNA double-strand breaks, but its functions in repair by nonhomologous end joining (NHEJ) pathways are poorly understood. We have investigated requirements for MRN in class switch recombination (CSR), a programmed DNA rearrangement in B lymphocytes that ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1639

    authors： Dinkelmann M,Spehalski E,Stoneham T,Buis J,Wu Y,Sekiguchi JM,Ferguson DO

    更新日期：2009-08-01 00:00:00

  • RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1.

    abstract：:Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-020-0393-9

    authors： Matsuo Y,Tesina P,Nakajima S,Mizuno M,Endo A,Buschauer R,Cheng J,Shounai O,Ikeuchi K,Saeki Y,Becker T,Beckmann R,Inada T

    更新日期：2020-04-01 00:00:00

  • DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation.

    abstract：:Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27 to mark genes for repression. We measured the dynamics of PRC2 binding on recombinant chromatin and free DNA at the single-molecule level using total internal reflection fluorescence (TIRF) microscopy. PRC2 preferentially binds free DNA with mu...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.3488

    authors： Choi J,Bachmann AL,Tauscher K,Benda C,Fierz B,Müller J

    更新日期：2017-12-01 00:00:00

  • Developmental programming of CpG island methylation profiles in the human genome.

    abstract：:CpG island-like sequences are commonly thought to provide the sole signals for designating constitutively unmethylated regions in the genome, thus generating open chromatin domains within a sea of global repression. Using a new database obtained from comprehensive microarray analysis, we show that unmethylated regions...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1594

    authors： Straussman R,Nejman D,Roberts D,Steinfeld I,Blum B,Benvenisty N,Simon I,Yakhini Z,Cedar H

    更新日期：2009-05-01 00:00:00

  • A teacupful of medicine?

    abstract：:Green tea has held a long-standing place in traditional Asian medicine. Scientific research is now beginning to explain why. ...

    journal_title：Nature structural & molecular biology

    pub_type： 评论,社论

    doi：10.1038/nsmb0608-537

    authors：

    更新日期：2008-06-01 00:00:00

  • Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation.

    abstract：:We have isolated a soluble cytochrome from Shewanella oneidensis that contains eight covalently attached heme groups and determined its crystal structure. One of these hemes exhibits novel ligation of the iron atom by the epsilon-amino group of a lysine residue, despite its attachment via a typical CXXCH motif. This h...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb827

    authors： Mowat CG,Rothery E,Miles CS,McIver L,Doherty MK,Drewette K,Taylor P,Walkinshaw MD,Chapman SK,Reid GA

    更新日期：2004-10-01 00:00:00

  • Author Correction: H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming.

    abstract：:In this article, the Ponceau staining presented in Fig. 1b (right, bottom) does not follow best practices for figure preparation since itinadvertently included duplications from the Ponceau staining presented in Supplementary Fig. 1b (for which the same preparation ofnucleosomes from HeLa cells had been used). A new F...

    journal_title：Nature structural & molecular biology

    pub_type： 已发布勘误

    doi：10.1038/s41594-018-0090-0

    authors： Daujat S,Weiss T,Mohn F,Lange UC,Ziegler-Birling C,Zeissler U,Lappe M,Schübeler D,Torres-Padilla ME,Schneider R

    更新日期：2018-08-01 00:00:00

  • Transcription promotes contraction of CAG repeat tracts in human cells.

    abstract：:Induced transcription through CAG repeats in human cells increases repeat contraction approximately 15-fold in both confluent and proliferating cells. Repeats are stabilized against contraction by siRNA knockdown of MSH2, MSH3 or XPA, but not by knockdown of MSH6, XPC or FEN1. These results define a pathway for CAG.CT...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb1042

    authors： Lin Y,Dion V,Wilson JH

    更新日期：2006-02-01 00:00:00

  • Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses.

    abstract：:Methylation of histones is central to chromatin regulation, and thus previously unknown mechanisms regulating genome function can be revealed through the discovery of new histone methyl marks. Here we identify Set5 as the first histone H4 methyltransferase, which monomethylates the critical H4 lysine residues 5, 8 and...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2252

    authors： Green EM,Mas G,Young NL,Garcia BA,Gozani O

    更新日期：2012-02-19 00:00:00

  • An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.

    abstract：:Many viruses bypass canonical cap-dependent translation in host cells by using internal ribosomal entry sites (IRESs) in their transcripts; IRESs hijack initiation factors for the assembly of initiation complexes. However, it is currently unknown how IRES RNAs recognize initiation factors that have no endogenous RNA b...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.3280

    authors： Imai S,Kumar P,Hellen CU,D'Souza VM,Wagner G

    更新日期：2016-09-01 00:00:00

  • Allosteric inhibition of antiapoptotic MCL-1.

    abstract：:MCL-1 is an antiapoptotic BCL-2 family protein that has emerged as a major pathogenic factor in human cancer. Like BCL-2, MCL-1 bears a surface groove whose function is to sequester the BH3 killer domains of proapoptotic BCL-2 family members, a mechanism harnessed by cancer cells to establish formidable apoptotic bloc...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.3223

    authors： Lee S,Wales TE,Escudero S,Cohen DT,Luccarelli J,Gallagher CG,Cohen NA,Huhn AJ,Bird GH,Engen JR,Walensky LD

    更新日期：2016-06-01 00:00:00

  • Structure and mechanism of the RNA polymerase II transcription machinery.

    abstract：:Advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a marked increase in the understanding of the mechanism of transcription. Models for the specific assembly of the RNA polymerase II transcription machinery at a promoter, conformational changes that occur during ini...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章,评审

    doi：10.1038/nsmb763

    authors： Hahn S

    更新日期：2004-05-01 00:00:00

  • Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs.

    abstract：:Flavin-containing monooxygenases (FMOs) are ubiquitous in all domains of life and metabolize a myriad of xenobiotics, including toxins, pesticides and drugs. However, despite their pharmacological importance, structural information remains bereft. To further our understanding behind their biochemistry and diversity, w...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0347-2

    authors： Nicoll CR,Bailleul G,Fiorentini F,Mascotti ML,Fraaije MW,Mattevi A

    更新日期：2020-01-01 00:00:00

  • Let K-Ras activate its own inhibitor.

    abstract：: ...

    journal_title：Nature structural & molecular biology

    pub_type： 新闻

    doi：10.1038/s41594-018-0066-0

    authors： Statsyuk AV

    更新日期：2018-06-01 00:00:00

  • Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases.

    abstract：:Kinases are involved in disease development and modulation of their activity can be therapeutically beneficial. Drug-resistant mutant kinases are valuable tools in drug discovery efforts, but the prediction of mutants across the kinome is challenging. Here, we generate deep mutational scanning data to identify mutant ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0358-z

    authors： Persky NS,Hernandez D,Do Carmo M,Brenan L,Cohen O,Kitajima S,Nayar U,Walker A,Pantel S,Lee Y,Cordova J,Sathappa M,Zhu C,Hayes TK,Ram P,Pancholi P,Mikkelsen TS,Barbie DA,Yang X,Haq R,Piccioni F,Root DE,Johannes

    更新日期：2020-01-01 00:00:00

  • The opening of the two pores of the Hv1 voltage-gated proton channel is tuned by cooperativity.

    abstract：:In voltage-gated sodium, potassium and calcium channels, the functions of ion conduction and voltage sensing are performed by two distinct structural units: the pore domain and the voltage-sensing domain (VSD). In the hydrogen voltage-gated channel 1 (Hv1), the VSD, unusually, performs both functions. Hv1 was recently...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1738

    authors： Tombola F,Ulbrich MH,Kohout SC,Isacoff EY

    更新日期：2010-01-01 00:00:00

  • An asymmetric interface between the regulatory and core particles of the proteasome.

    abstract：:The Saccharomyces cerevisiae proteasome comprises a 19-subunit regulatory particle and a 28-subunit core particle. To be degraded, substrates must cross the core particle-regulatory particle interface, a site for complex conformational changes and regulatory events. This interface includes two aligned heteromeric ring...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2147

    authors： Tian G,Park S,Lee MJ,Huck B,McAllister F,Hill CP,Gygi SP,Finley D

    更新日期：2011-10-30 00:00:00

  • Nemo kinase phosphorylates β-catenin to promote ommatidial rotation and connects core PCP factors to E-cadherin-β-catenin.

    abstract：:Frizzled planar cell polarity (PCP) signaling regulates cell motility in several tissues, including ommatidial rotation in Drosophila melanogaster. The Nemo kinase (Nlk in vertebrates) has also been linked to cell-motility regulation and ommatidial rotation but its mechanistic role(s) during rotation remain obscure. W...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2049

    authors： Mirkovic I,Gault WJ,Rahnama M,Jenny A,Gaengel K,Bessette D,Gottardi CJ,Verheyen EM,Mlodzik M

    更新日期：2011-06-01 00:00:00

  • Structural basis for -10 promoter element melting by environmentally induced sigma factors.

    abstract：:Bacterial transcription is controlled by sigma factors, the RNA polymerase subunits that act as initiation factors. Although a single housekeeping sigma factor enables transcription from thousands of promoters, environmentally induced sigma factors redirect gene expression toward small regulons to carry out focused re...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2777

    authors： Campagne S,Marsh ME,Capitani G,Vorholt JA,Allain FH

    更新日期：2014-03-01 00:00:00

  • Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.

    abstract：:HIV-1 capsid plays multiple key roles in viral replication, and inhibition of capsid assembly is an attractive target for therapeutic intervention. Here, we report the atomic-resolution structure of capsid protein (CA) tubes, determined by magic-angle spinning NMR and data-guided molecular dynamics simulations. Functi...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-020-0489-2

    authors： Lu M,Russell RW,Bryer AJ,Quinn CM,Hou G,Zhang H,Schwieters CD,Perilla JR,Gronenborn AM,Polenova T

    更新日期：2020-09-01 00:00:00

  • The RNA exosome promotes transcription termination of backtracked RNA polymerase II.

    abstract：:The exosome is an RNA-decay complex that constantly monitors transcription and contributes to post-transcriptional turnover of faulty mRNAs. Yet how nuclear RNA surveillance by the exosome is coordinated with transcription is still unknown. Here we show that the RNA exosome of Schizosaccharomyces pombe can target the ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2893

    authors： Lemay JF,Larochelle M,Marguerat S,Atkinson S,Bähler J,Bachand F

    更新日期：2014-10-01 00:00:00

  • A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.

    abstract：:Interactions between Src homology 2 (SH2) domains and phosphotyrosine sites regulate tyrosine kinase signaling networks. Selective perturbation of these interactions is challenging due to the high homology among the 120 human SH2 domains. Using an improved phage-display selection system, we generated a small antibody ...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1793

    authors： Wojcik J,Hantschel O,Grebien F,Kaupe I,Bennett KL,Barkinge J,Jones RB,Koide A,Superti-Furga G,Koide S

    更新日期：2010-04-01 00:00:00

  • Structure of the measles virus hemagglutinin bound to the CD46 receptor.

    abstract：:The highly contagious measles virus infects millions of individuals worldwide, causing serious disease in children of developing countries. Infection is initiated by attachment of the measles virus hemagglutinin (MV-H), a glycoprotein anchored to the virus envelope, to the host cell receptors CD46 or signaling lymphoc...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.1726

    authors： Santiago C,Celma ML,Stehle T,Casasnovas JM

    更新日期：2010-01-01 00:00:00

  • The tail structure of bacteriophage T4 and its mechanism of contraction.

    abstract：:Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fiber...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb975

    authors： Kostyuchenko VA,Chipman PR,Leiman PG,Arisaka F,Mesyanzhinov VV,Rossmann MG

    更新日期：2005-09-01 00:00:00

  • Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM.

    abstract：:The eukaryotic exosome is a multisubunit complex typically composed of a catalytically inactive core and the Rrp44 protein, which contains 3'-to-5' exo- and endo-RNase activities. RNA substrates have been shown to be recruited through the core to reach Rrp44's exo-RNase (EXO) site. Using single-particle EM and biochem...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2736

    authors： Liu JJ,Bratkowski MA,Liu X,Niu CY,Ke A,Wang HW

    更新日期：2014-01-01 00:00:00

  • BAK core dimers bind lipids and can be bridged by them.

    abstract：:BAK and BAX are essential mediators of apoptosis that oligomerize in response to death cues, thereby causing permeabilization of the mitochondrial outer membrane. Their transition from quiescent monomers to pore-forming oligomers involves a well-characterized symmetric dimer intermediate. However, no essential seconda...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-020-0494-5

    authors： Cowan AD,Smith NA,Sandow JJ,Kapp EA,Rustam YH,Murphy JM,Brouwer JM,Bernardini JP,Roy MJ,Wardak AZ,Tan IK,Webb AI,Gulbis JM,Smith BJ,Reid GE,Dewson G,Colman PM,Czabotar PE

    更新日期：2020-11-01 00:00:00

  • Structural basis of the proinflammatory signaling complex mediated by TSLP.

    abstract：:Thymic stromal lymphopoietin (TSLP), a cytokine produced by epithelial cells at barrier surfaces, is pivotal for the development of widespread chronic inflammatory disorders such as asthma and atopic dermatitis. The structure of the mouse TSLP-mediated signaling complex reveals how TSLP establishes extensive interface...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2794

    authors： Verstraete K,van Schie L,Vyncke L,Bloch Y,Tavernier J,Pauwels E,Peelman F,Savvides SN

    更新日期：2014-04-01 00:00:00

  • Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP.

    abstract：:The cyclic enzymatic removal and ligation of the C-terminal tyrosine of α-tubulin generates heterogeneous microtubules and affects their functions. Here we describe the crystal and solution structure of the tubulin carboxypeptidase complex between vasohibin (VASH1) and small vasohibin-binding protein (SVBP), which fol...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/s41594-019-0254-6

    authors： Adamopoulos A,Landskron L,Heidebrecht T,Tsakou F,Bleijerveld OB,Altelaar M,Nieuwenhuis J,Celie PHN,Brummelkamp TR,Perrakis A

    更新日期：2019-07-01 00:00:00

  • Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells.

    abstract：:The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs undergoing premature termination of translation. It has been argued that in human cells, NMD is restricted to a pioneer round of translation initiated on mRNAs associated with the cap-binding complex (CBC) and that the exchange of the CBC for the eIF4F tran...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb.2575

    authors： Durand S,Lykke-Andersen J

    更新日期：2013-06-01 00:00:00

  • Ligand-induced rearrangement of the dimeric metabotropic glutamate receptor 1alpha.

    abstract：:The extracellular domain of the metabotropic glutamate receptor 1alpha (mGluR1alpha) forms a dimer and the ligand, glutamate, induces a structural rearrangement in this domain. However, the conformational change in the cytoplasmic domain, which is critical for mGluR1alpha's interaction with G proteins, remains unclear...

    journal_title：Nature structural & molecular biology

    pub_type： 杂志文章

    doi：10.1038/nsmb770

    authors： Tateyama M,Abe H,Nakata H,Saito O,Kubo Y

    更新日期：2004-07-01 00:00:00