RNA–protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins

(2018) Daniel Maticzka et al.   Nature Communications

Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling

(2018) Ayala Shiber et al.   NATURE

Protein complexes assemble as they are being made

(2018) Christine Mayr   NATURE

mRNA interactome capture in mammalian cells

(2017) Nicolai Kastelic et al.   METHODS

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding

(2017) Bagdeser A. Ozdilek et al.   NUCLEIC ACIDS RESEARCH

LncRNA MEG3 downregulation mediated by DNMT3b contributes to nickel malignant transformation of human bronchial epithelial cells via modulating PHLPP1 transcription and HIF-1α translation

(2017) C Zhou et al.   ONCOGENE

Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination

(2017) Nana Diarra dit Konté et al.   Nature Communications

Local Nucleation of Microtubule Bundles through Tubulin Concentration into a Condensed Tau Phase

(2017) Amayra Hernández-Vega et al.   Cell Reports

Advances and challenges in the detection of transcriptome-wide protein-RNA interactions

(2017) Emily C. Wheeler et al.   Wiley Interdisciplinary Reviews-RNA

The new (dis)order in RNA regulation

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

Steroid receptor RNA activator: Biologic function and role in disease

(2016) Chan Liu et al.   CLINICA CHIMICA ACTA

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

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

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

An inducible long noncoding RNA amplifies DNA damage signaling

(2016) Adam M Schmitt et al.   NATURE GENETICS

MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences

(2016) Nawar Malhis et al.   NUCLEIC ACIDS RESEARCH

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

Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq

(2016) Cindo O. Nicholson et al.   RNA

Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

(2016) Sneha Nishtala et al.   Scientific Reports

catRAPIDsignature: identification of ribonucleoproteins and RNA-binding regions

(2015) Carmen Maria Livi et al.   BIOINFORMATICS

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

(2015) Bodu Liu et al.   CANCER CELL

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

It’s Raining Liquids: RNA Tunes Viscoelasticity and Dynamics of Membraneless Organelles

(2015) Lin Guo et al.   MOLECULAR CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function

(2015) Tetsuro Murakami et al.   NEURON

Induced folding in RNA recognition byArabidopsis thalianaDCL1

(2015) Irina P. Suarez et al.   NUCLEIC ACIDS RESEARCH

The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2

(2015) Chen Davidovich et al.   RNA

Emerging Roles of Disordered Sequences in RNA-Binding Proteins

(2015) Sara Calabretta 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

Extreme multifunctional proteins identified from a human protein interaction network

(2015) Charles E. Chapple et al.   Nature Communications

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

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

The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein

(2015) Michael R. White et al.   Wiley Interdisciplinary Reviews-RNA

Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

(2015) Sonja Kroschwald et al.   eLife

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins

(2015) Mihaly Varadi et al.   PLoS One

Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport

(2015) Silpi Banerjee et al.   RNA Biology

High-throughput characterization of protein-RNA interactions

(2014) K. B. Cook et al.   Briefings in Functional Genomics

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Advantages of proteins being disordered

(2014) Zhirong Liu et al.   PROTEIN SCIENCE

The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation

(2014) P. Wang et al.   SCIENCE

Constitutive patterns of gene expression regulated by RNA-binding proteins

(2014) Davide Cirillo et al.   GENOME BIOLOGY

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

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

(2013) Zhenling Peng et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNA in the Loop

(2013) Johnny T.Y. Kung et al.   DEVELOPMENTAL CELL

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

A decade and a half of protein intrinsic disorder: Biology still waits for physics

(2013) Vladimir N. Uversky   PROTEIN SCIENCE

Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins

(2013) ShengQi Xiang et al.   STRUCTURE

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

CRAC: an integrated approach to the analysis of RNA-seq reads

(2013) Nicolas Philippe et al.   GENOME BIOLOGY

Human intronless genes: Functional groups, associated diseases, evolution, and mRNA processing in absence of splicing

(2012) Ewa A. Grzybowska   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2012) Masato Kato et al.   CELL

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

(2012) Alfredo Castello et al.   CELL

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Transcriptome-wide Analysis of Exosome Targets

(2012) Claudia Schneider et al.   MOLECULAR CELL

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

(2012) Eva Matoulkova et al.   RNA Biology

Intrinsic Disorder in the Human Spliceosomal Proteome

(2012) Iga Korneta et al.   PLoS Computational Biology

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

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

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

The diverse functions of GAPDH: Views from different subcellular compartments

(2010) Carlos Tristan et al.   CELLULAR SIGNALLING

SVM based prediction of RNA-binding proteins using binding residues and evolutionary information

(2010) Manish Kumar et al.   JOURNAL OF MOLECULAR RECOGNITION

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

The REM phase of gene regulation

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

Close encounters of the third kind: disordered domains and the interactions of proteins

(2009) Peter Tompa et al.   BIOESSAYS

HuR recruits let-7/RISC to repress c-Myc expression

(2009) H. H. Kim et al.   GENES & DEVELOPMENT

How Common Are Extraribosomal Functions of Ribosomal Proteins?

(2009) Jonathan R. Warner et al.   MOLECULAR CELL

RNA recognition motifs: boring? Not quite

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

The functional duality of iron regulatory protein 1

(2008) Karl Volz   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure and function of KH domains

(2008) Roberto Valverde et al.   FEBS Journal

Identification of a signature motif in target mRNAs of RNA-binding protein AUF1

(2008) Krystyna Mazan-Mamczarz et al.   NUCLEIC ACIDS RESEARCH