Translatome profiling: methods for genome-scale analysis of mRNA translation

Genome-wide profiling reveals a role for T-cell intracellular antigens TIA1 and TIAR in the control of translational specificity in HeLa cells

(2015) Isabel Carrascoso et al.   BIOCHEMICAL JOURNAL

Molecular Profiling of Neurons Based on Connectivity

(2014) Mats I. Ekstrand et al.   CELL

A Bicistronic MAVS Transcript Highlights a Class of Truncated Variants in Antiviral Immunity

(2014) Sky W. Brubaker et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

(2014) Anton Kratz et al.   GENOME RESEARCH

Cell-specific translational profiling in acute kidney injury

(2014) Jing Liu et al.   JOURNAL OF CLINICAL INVESTIGATION

Structural basis for the inhibition of the eukaryotic ribosome

(2014) Nicolas Garreau de Loubresse et al.   NATURE

Translational control of immune responses: from transcripts to translatomes

(2014) Ciriaco A Piccirillo et al.   NATURE IMMUNOLOGY

Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP)

(2014) Myriam Heiman et al.   Nature Protocols

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

In vivo radiation response of proneural glioma characterized by protective p53 transcriptional program and proneural-mesenchymal shift

(2014) J. Halliday et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational Regulation of Specific mRNAs Controls Feedback Inhibition and Survival during Macrophage Activation

(2014) Johanna Schott et al.   PLoS Genetics

KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

(2014) Carolina Arias et al.   PLoS Pathogens

Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression

(2013) Flora Picard et al.   BMC GENOMICS

Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates

(2013) F. V. Karginov et al.   GENES & DEVELOPMENT

A perspective on mammalian upstream open reading frame function

(2013) Joanna Somers et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A role for eukaryotic initiation factor 4B overexpression in the pathogenesis of diffuse large B-cell lymphoma

(2013) E Horvilleur et al.   LEUKEMIA

Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes

(2013) Botao Liu et al.   MOLECULAR CELL

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

Widespread Regulation of Translation by Elongation Pausing in Heat Shock

(2013) Reut Shalgi et al.   MOLECULAR CELL

Structures of the human and Drosophila 80S ribosome

(2013) Andreas M. Anger et al.   NATURE

Evaluation of TRAP-sequencing technology with a versatile conditional mouse model

(2013) Mike Hupe et al.   NUCLEIC ACIDS RESEARCH

Analysis of Genome-Wide Changes in the Translatome of Arabidopsis Seedlings Subjected to Heat Stress

(2013) Emilio Yángüez et al.   PLoS One

Heat Shock Modulates Neutrophil Motility in Zebrafish

(2013) Pui-ying Lam et al.   PLoS One

Interrogating translational efficiency and lineage-specific transcriptomes using ribosome affinity purification

(2013) P. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational profiling of cardiomyocytes identifies an early Jak1/Stat3 injury response required for zebrafish heart regeneration

(2013) Y. Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polysome profiling shows extensive posttranscriptional regulation during human adipocyte stem cell differentiation into adipocytes

(2013) Lucia Spangenberg et al.   Stem Cell Research

Conserved Translatome Remodeling in Nematode Species Executing a Shared Developmental Transition

(2013) Michael Stadler et al.   PLoS Genetics

Integrative “Omics”-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses

(2013) Bork A. Berghoff et al.   PLoS Genetics

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale

(2013) Audrey M. Michel et al.   Wiley Interdisciplinary Reviews-RNA

Local Translation of Extranuclear Lamin B Promotes Axon Maintenance

(2012) Byung C. Yoon et al.   CELL

LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells

(2012) Jun Cho et al.   CELL

Cell type-specific translational profiling in theXenopus laevisretina

(2012) F. L. Watson et al.   DEVELOPMENTAL DYNAMICS

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Reduced Expression of Ribosomal Proteins Relieves MicroRNA-Mediated Repression

(2012) Maja M. Janas et al.   MOLECULAR CELL

A unifying model for mTORC1-mediated regulation of mRNA translation

(2012) Carson C. Thoreen et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Sustained translational repression by eIF2α-P mediates prion neurodegeneration

(2012) Julie A. Moreno et al.   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

(2012) Marek Zywicki et al.   NUCLEIC ACIDS RESEARCH

A Versatile Method for Cell-Specific Profiling of Translated mRNAs in Drosophila

(2012) Amanda Thomas et al.   PLoS One

Monitoring cotranslational protein folding in mammalian cells at codon resolution

(2012) Y. Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct perturbation of the translatome by the antidiabetic drug metformin

(2012) O. Larsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

(2012) M. V. Gerashchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential association of microRNAs with polysomes reflects distinct strengths of interactions with their mRNA targets

(2012) N. Molotski et al.   RNA

IRES-dependent translation of egr2 is induced under inflammatory conditions

(2012) D. Rubsamen et al.   RNA

Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

(2012) A. A. Bazzini et al.   SCIENCE

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Translational Control in Cancer Etiology

(2012) D. Ruggero   Cold Spring Harbor Perspectives in Biology

The Structure and Function of the Eukaryotic Ribosome

(2012) D. N. Wilson et al.   Cold Spring Harbor Perspectives in Biology

Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells

(2012) Alexandra Dana et al.   PLoS Computational Biology

Mechanisms and implications of programmed translational frameshifting

(2012) Jonathan D. Dinman   Wiley Interdisciplinary Reviews-RNA

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Protein Expression Regulation under Oxidative Stress

(2011) Christine Vogel et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

The role of IREStrans-acting factors in regulating translation initiation

(2010) Helen A. King et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

(2010) Yuling Jiao et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins

(2010) Andrew G. Cridge et al.   NUCLEIC ACIDS RESEARCH

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Translational reprogramming following UVB irradiation is mediated by DNA-PKcs and allows selective recruitment to the polysomes of mRNAs encoding DNA repair enzymes

(2009) I. R. Powley et al.   GENES & DEVELOPMENT

Affinity purification of ribosomes to access the translatome

(2009) Regula E. Halbeisen et al.   METHODS

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Stress-Dependent Coordination of Transcriptome and Translatome in Yeast

(2009) Regula E Halbeisen et al.   PLOS BIOLOGY

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL