A brave new world of RNA-binding proteins

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

(2017) Vladimir Despic et al.   GENOME RESEARCH

Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification

(2017) Meeli Mullari et al.   JOURNAL OF PROTEOME RESEARCH

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

(2017) Thomas Treiber et al.   MOLECULAR CELL

m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition

(2017) Boxuan Simen Zhao et al.   NATURE

Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation

(2017) Niels H. Gehring et al.   TRENDS IN BIOCHEMICAL SCIENCES

Comprehensive Identification of mRNA-Binding Proteins of Leishmania donovani by Interactome Capture

(2017) Devki Nandan et al.   PLoS One

The specificity of long noncoding RNA expression

(2016) Brian S. Gloss et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The new (dis)order in RNA regulation

(2016) Aino I. Järvelin et al.   Cell Communication and Signaling

A structural perspective of RNA recognition by intrinsically disordered proteins

(2016) Sushmita Basu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Determinants of affinity and specificity in RNA-binding proteins

(2016) Stephanie Helder et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An RNA‐binding atypical tropomyosin recruits kinesin‐1 dynamically to oskar mRNPs

(2016) Imre Gáspár et al.   EMBO JOURNAL

The mRNA-bound proteome of the early fly embryo

(2016) Hans-Hermann Wessels et al.   GENOME RESEARCH

Identification of RNA-binding Proteins in Macrophages by Interactome Capture

(2016) Anke Liepelt et al.   MOLECULAR & CELLULAR PROTEOMICS

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells

(2016) Chongsheng He et al.   MOLECULAR CELL

Resources for the Comprehensive Discovery of Functional RNA Elements

(2016) Balaji Sundararaman et al.   MOLECULAR CELL

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes

(2016) Kristopher W. Brannan et al.   MOLECULAR CELL

Gene expression regulatory networks inTrypanosoma brucei: insights into the role of the mRNA-binding proteome

(2016) Smiths Lueong et al.   MOLECULAR MICROBIOLOGY

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions

(2016) Benedikt M. Beckmann et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings

(2016) Marlene Reichel et al.   PLANT CELL

UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts

(2016) Zhicheng Zhang et al.   Plant Methods

Cyclin A2 is an RNA binding protein that controls Mre11 mRNA translation

(2016) A. Kanakkanthara et al.   SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

The Spliceosome: The Ultimate RNA Chaperone and Sculptor

(2016) Panagiotis Papasaikas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Principles and Properties of Stress Granules

(2016) David S.W. Protter et al.   TRENDS IN CELL BIOLOGY

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

(2016) Vasiliy O. Sysoev et al.   Nature Communications

Serial interactome capture of the human cell nucleus

(2016) Thomas Conrad et al.   Nature Communications

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

(2016) Yalin Liao et al.   Cell Reports

The organization and regulation of mRNA-protein complexes

(2016) Olivia S. Rissland   Wiley Interdisciplinary Reviews-RNA

Translating the epitranscriptome

(2016) Thomas Philipp Hoernes et al.   Wiley Interdisciplinary Reviews-RNA

The RNA-binding protein repertoire of Arabidopsis thaliana

(2016) Claudius Marondedze et al.   Scientific Reports

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

(2015) Guramrit Singh et al.   Annual Review of Biochemistry

Structural Snapshots of Actively Translating Human Ribosomes

(2015) Elmar Behrmann et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Genome-Wide Identification of Fas/CD95 Alternative Splicing Regulators Reveals Links with Iron Homeostasis

(2015) J. Ramón Tejedor et al.   MOLECULAR CELL

Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

(2015) Panagiotis Papasaikas et al.   MOLECULAR CELL

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Conserved mRNA-binding proteomes in eukaryotic organisms

(2015) Ana M Matia-González et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular insights into HSD10 disease: impact of SDR5C1 mutations on the human mitochondrial RNase P complex

(2015) Elisa Vilardo et al.   NUCLEIC ACIDS RESEARCH

FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

(2015) Johannes Popow et al.   RNA

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness

(2015) G. Manokaran et al.   SCIENCE

Probing RNA–protein networks: biochemistry meets genomics

(2015) Zachary T. Campbell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins

(2015) Alfredo Castello et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3

(2015) Anna Gebhardt et al.   Nature Communications

Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution

(2015) Nick Quade et al.   Nature Communications

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

(2015) Benedikt M. Beckmann et al.   Nature Communications

Conserved mRNA-binding proteomes in eukaryotic organisms

(2015) Ana M Matia-González et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis

(2015) Hana Antonicka et al.   Cell Reports

Cytoplasmic sensing of viral nucleic acids

(2015) Matthias Habjan et al.   Current Opinion in Virology

Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression

(2015) Jorge Boucas et al.   PLoS One

The Ribosome Emerges from a Black Box

(2014) V. Ramakrishnan   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Nascent RNA interaction keeps PRC2 activity poised and in check

(2014) Syuzo Kaneko et al.   GENES & DEVELOPMENT

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Roles of 17β-hydroxysteroid dehydrogenase type 10 in neurodegenerative disorders

(2014) Song-Yu Yang et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Mechanism of Dis3l2 substrate recognition in the Lin28–let-7 pathway

(2014) Christopher R. Faehnle et al.   NATURE

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

A day in the life of the spliceosome

(2014) A. Gregory Matera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The structure, function and evolution of proteins that bind DNA and RNA

(2014) William H. Hudson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of novel non-canonical RNA-binding sites in Gemin5 involved in internal initiation of translation

(2014) Javier Fernandez-Chamorro et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

mRNP granules

(2014) J Ross Buchan   RNA Biology

A versatile assay for RNA-binding proteins in living cells

(2014) C. Strein et al.   RNA

The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production

(2014) E. G. Chapman et al.   SCIENCE

Trim25 Is an RNA-Specific Activator of Lin28a/TuT4-Mediated Uridylation

(2014) Nila Roy Choudhury et al.   Cell Reports

Emerging mechanisms of mRNP remodeling regulation

(2014) Chyi-Ying A. Chen et al.   Wiley Interdisciplinary Reviews-RNA

Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite

(2014) Carina C Clingman et al.   eLife

The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding

(2013) Fabio Casu et al.   BIOPHYSICAL JOURNAL

Posttranscriptional Control of T Cell Effector Function by Aerobic Glycolysis

(2013) Chih-Hao Chang et al.   CELL

RNA sensing: the more RIG-I the merrier?

(2013) Jan Rehwinkel   EMBO REPORTS

Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

(2013) D. M. Klass et al.   GENOME RESEARCH

The “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions

(2013) Kasandra J. Riley et al.   MOLECULAR CELL

Defining the RGG/RG Motif

(2013) Palaniraja Thandapani et al.   MOLECULAR CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

System-wide identification of RNA-binding proteins by interactome capture

(2013) Alfredo Castello et al.   Nature Protocols

How cells get the message: dynamic assembly and function of mRNA–protein complexes

(2013) Michaela Müller-McNicoll et al.   NATURE REVIEWS GENETICS

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate

(2013) Suzanne R. Lee et al.   TRENDS IN CELL BIOLOGY

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Investigation of protein–RNA interactions by mass spectrometry—Techniques and applications

(2012) Carla Schmidt et al.   Journal of Proteomics

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Global analysis of yeast mRNPs

(2012) Sarah F Mitchell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The protein acetylome and the regulation of metabolism

(2012) Shufan Xing et al.   TRENDS IN PLANT SCIENCE

dsRNA-Dependent Protein Kinase PKR and its Role in Stress, Signaling and HCV Infection

(2012) Stéphanie Dabo et al.   Viruses-Basel

From Cis-Regulatory Elements to Complex RNPs and Back

(2012) F. Gebauer et al.   Cold Spring Harbor Perspectives in Biology

CWC22 Connects Pre-mRNA Splicing and Exon Junction Complex Assembly

(2012) Anna-Lena Steckelberg et al.   Cell Reports

TGF-β induces the expression of the adaptor Ndfip1 to silence IL-4 production during iTreg cell differentiation

(2011) Allison M Beal et al.   NATURE IMMUNOLOGY

From unwinding to clamping — the DEAD box RNA helicase family

(2011) Patrick Linder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction

(2011) Anh Tuân Phan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phosphorylation of glutamyl-prolyl tRNA synthetase by cyclin-dependent kinase 5 dictates transcript-selective translational control

(2011) A. Arif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Posttranscriptional regulation in Drosophila oocytes and early embryos

(2011) Paul Lasko   Wiley Interdisciplinary Reviews-RNA

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

The diverse functions of GAPDH: Views from different subcellular compartments

(2010) Carlos Tristan et al.   CELLULAR SIGNALLING

A non-enzymatic function of 17β-hydroxysteroid dehydrogenase type 10 is required for mitochondrial integrity and cell survival

(2010) Katharina Rauschenberger et al.   EMBO Molecular Medicine

Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA

(2010) S. Kaneko et al.   GENES & DEVELOPMENT

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

(2010) Nikoleta G. Tsvetanova et al.   PLoS One

A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

(2010) Tanja Scherrer et al.   PLoS One

The REM phase of gene regulation

(2010) Matthias W. Hentze et al.   TRENDS IN BIOCHEMICAL SCIENCES

Aptamers and the RNA World, Past and Present

(2010) L. Gold et al.   Cold Spring Harbor Perspectives in Biology

Searching DNA via a “Monkey Bar” Mechanism: The Significance of Disordered Tails

(2009) Dana Vuzman et al.   JOURNAL OF MOLECULAR BIOLOGY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

Two-Site Phosphorylation of EPRS Coordinates Multimodal Regulation of Noncanonical Translational Control Activity

(2009) Abul Arif et al.   MOLECULAR CELL

RNA granules: post-transcriptional and epigenetic modulators of gene expression

(2009) Paul Anderson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites

(2009) S. de Breyne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FASTKD2 Nonsense Mutation in an Infantile Mitochondrial Encephalomyopathy Associated with Cytochrome C Oxidase Deficiency

(2008) Daniele Ghezzi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme

(2008) Johann Holzmann et al.   CELL

RNA recognition motifs: boring? Not quite

(2008) Antoine Cléry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure and function of KH domains

(2008) Roberto Valverde et al.   FEBS Journal

Glyceraldehyde-3-Phosphate Dehydrogenase Regulates Endothelin-1 Expression by a Novel, Redox-Sensitive Mechanism Involving mRNA Stability

(2008) F. Rodriguez-Pascual et al.   MOLECULAR AND CELLULAR BIOLOGY

DAPK-ZIPK-L13a Axis Constitutes a Negative-Feedback Module Regulating Inflammatory Gene Expression

(2008) Rupak Mukhopadhyay et al.   MOLECULAR CELL

A structural understanding of the dynamic ribosome machine

(2008) Thomas A. Steitz   NATURE REVIEWS MOLECULAR CELL BIOLOGY