Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases

Can we observe changes in mRNA “state”? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related processes

(2016) C. Zurla et al.   ANALYST

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

(2016) Martyna O. Urbanek et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

RNA FISH for detecting expanded repeats in human diseases

(2016) Martyna O. Urbanek et al.   METHODS

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

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

The biogenesis and emerging roles of circular RNAs

(2016) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Serial interactome capture of the human cell nucleus

(2016) Thomas Conrad et al.   Nature Communications

Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival

(2016) Anne E. Conway et al.   Cell Reports

RNA Whole-Mount In situ Hybridisation Proximity Ligation Assay (rISH-PLA), an Assay for Detecting RNA-Protein Complexes in Intact Cells

(2016) Ioannis M. Roussis et al.   PLoS One

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

(2015) Jakub Kochan et al.   BIOTECHNIQUES

The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner

(2015) Nitzan Samra et al.   BMC MOLECULAR BIOLOGY

Proximity ligation assays of protein and RNA interactions in the male-specific lethal complex on Drosophila melanogaster polytene chromosomes

(2015) Henrik Lindehell et al.   CHROMOSOMA

Curcumin potentiates the anti-leukemia effects of imatinib by downregulation of the AKT/mTOR pathway and BCR/ABL gene expression in Ph+ acute lymphoblastic leukemia

(2015) Yong Guo et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Isolation of Endogenously Assembled RNA-Protein Complexes Using Affinity Purification Based on Streptavidin Aptamer S1

(2015) Yangchao Dong et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Nuclear accumulation of mRNAs underlies G4C2-repeat-induced translational repression in a cellular model of C9orf72 ALS

(2015) S. Rossi et al.   JOURNAL OF CELL SCIENCE

The emerging role of lncRNAs in cancer

(2015) Maite Huarte   NATURE MEDICINE

Quantitative proteomics using SILAC: Principles, applications, and developments

(2015) Xiulan Chen et al.   PROTEOMICS

Identification and characterization of cellular proteins interacting with Hepatitis E virus untranslated regions

(2015) Mandar S. Paingankar et al.   VIRUS RESEARCH

Nuclear retention of full-length HTT RNA is mediated by splicing factors MBNL1 and U2AF65

(2015) Xin Sun et al.   Scientific Reports

C9ORF72 GGGGCC Expanded Repeats Produce Splicing Dysregulation which Correlates with Disease Severity in Amyotrophic Lateral Sclerosis

(2015) Johnathan Cooper-Knock et al.   PLoS One

Sequestration of multiple RNA recognition motif-containing proteins by C9orf72 repeat expansions

(2014) Johnathan Cooper-Knock et al.   BRAIN

Ribonomic approaches to study the RNA-binding proteome

(2014) Camilla Faoro et al.   FEBS LETTERS

Stem–loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly

(2014) Shalini Sharma et al.   GENES & DEVELOPMENT

Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease

(2014) Ranjan Batra et al.   MOLECULAR CELL

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

(2014) Aaron R. Haeusler et al.   NATURE

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

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

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling

(2014) Jacob M Tome et al.   NATURE METHODS

Myotonic Dystrophy

(2014) Charles A. Thornton   NEUROLOGIC CLINICS

DDX6 regulates sequestered nuclear CUG-expanded DMPK-mRNA in dystrophia myotonica type 1

(2014) O. J. Pettersson et al.   NUCLEIC ACIDS RESEARCH

MBNL proteins and their target RNAs, interaction and splicing regulation

(2014) Patryk Konieczny et al.   NUCLEIC ACIDS RESEARCH

RNA imaging in living cells – methods and applications

(2014) Martyna O Urbanek et al.   RNA Biology

Mass spectrometry-based relative quantification of proteins in precatalytic and catalytically active spliceosomes by metabolic labeling (SILAC), chemical labeling (iTRAQ), and label-free spectral count

(2014) C. Schmidt et al.   RNA

Circular RNAs: diversity of form and function

(2014) Erika Lasda et al.   RNA

Lin28a regulates neuronal differentiation and controls miR-9 production

(2014) Jakub S. Nowak et al.   Nature Communications

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

(2014) Nila Roy Choudhury et al.   Cell Reports

Dissecting the expression landscape of RNA-binding proteins in human cancers

(2014) Bobak Kechavarzi et al.   GENOME BIOLOGY

Methods for comprehensive experimental identification of RNA-protein interactions

(2014) Colleen A McHugh et al.   GENOME BIOLOGY

Fragile X-associated tremor/ataxia syndrome (FXTAS): pathology and mechanisms

(2013) Paul Hagerman   ACTA NEUROPATHOLOGICA

hnRNP A3 binds to GGGGCC repeats and is a constituent of p62-positive/TDP43-negative inclusions in the hippocampus of patients with C9orf72 mutations

(2013) Kohji Mori et al.   ACTA NEUROPATHOLOGICA

Modeling key pathological features of frontotemporal dementia with C9ORF72 repeat expansion in iPSC-derived human neurons

(2013) Sandra Almeida et al.   ACTA NEUROPATHOLOGICA

Expression of Expanded CAG Transcripts Triggers Nucleolar Stress in Huntington's Disease

(2013) Ho Tsoi et al.   CEREBELLUM

Tissue-specific control of brain-enriched miR-7 biogenesis

(2013) N. R. Choudhury et al.   GENES & DEVELOPMENT

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators

(2013) M. Scheibe et al.   GENOME RESEARCH

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 Disease-associated r(GGGGCC)nRepeat from theC9orf72Gene Forms Tract Length-dependent Uni- and Multimolecular RNA G-quadruplex Structures

(2013) Kaalak Reddy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TMPyP4 Porphyrin Distorts RNA G-quadruplex Structures of the Disease-associated r(GGGGCC)nRepeat of theC9orf72Gene and Blocks Interaction of RNA-binding Proteins

(2013) Bita Zamiri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs

(2013) Carly I. Dix et al.   JOURNAL OF CELL BIOLOGY

Mass spectrometry-based identification of proteins interacting with nucleic acids

(2013) A. Tacheny et al.   Journal of Proteomics

Advances in clinical and molecular understanding of the FMR1 premutation and fragile X-associated tremor/ataxia syndrome

(2013) Randi Hagerman et al.   LANCET NEUROLOGY

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

The RNA-binding protein repertoire of embryonic stem cells

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

RNA Toxicity from the ALS/FTD C9ORF72 Expansion Is Mitigated by Antisense Intervention

(2013) Christopher J. Donnelly et al.   NEURON

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins

(2013) Kathrin Leppek et al.   NUCLEIC ACIDS RESEARCH

RNA-protein analysis using a conditional CRISPR nuclease

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

Expanded GGGGCC repeat RNA associated with amyotrophic lateral sclerosis and frontotemporal dementia causes neurodegeneration

(2013) Z. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease

(2013) K. Sathasivam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting RNA Foci in iPSC-Derived Motor Neurons from ALS Patients with a C9ORF72 Repeat Expansion

(2013) D. Sareen et al.   Science Translational Medicine

Translation of HTT mRNA with expanded CAG repeats is regulated by the MID1–PP2A protein complex

(2013) Sybille Krauß et al.   Nature Communications

Sequestration of DROSHA and DGCR8 by Expanded CGG RNA Repeats Alters MicroRNA Processing in Fragile X-Associated Tremor/Ataxia Syndrome

(2013) Chantal Sellier et al.   Cell Reports

Hexanucleotide Repeats in ALS/FTD Form Length-Dependent RNA Foci, Sequester RNA Binding Proteins, and Are Neurotoxic

(2013) Youn-Bok Lee et al.   Cell Reports

Sequestration by IFIT1 Impairs Translation of 2′O-unmethylated Capped RNA

(2013) Matthias Habjan et al.   PLoS Pathogens

Co-aggregation of RNA binding proteins in ALS spinal motor neurons: evidence of a common pathogenic mechanism

(2012) Brian A. Keller et al.   ACTA NEUROPATHOLOGICA

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

(2012) Eric T. Wang et al.   CELL

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

(2012) Alfredo Castello et al.   CELL

The C9ORF72 expansion mutation is a common cause of ALS+/−FTD in Europe and has a single founder

(2012) Bradley N Smith et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The RNA-binding protein Staufen1 is increased in DM1 skeletal muscle and promotes alternative pre-mRNA splicing

(2012) Aymeric Ravel-Chapuis et al.   JOURNAL OF CELL BIOLOGY

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

(2012) Carla Schmidt et al.   Journal of Proteomics

Fifteen years of the yeast three-hybrid system: RNA–protein interactions under investigation

(2012) Franck Martin   METHODS

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

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

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Global analysis of yeast mRNPs

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

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

(2012) Deepak Balasubramanian et al.   NUCLEIC ACIDS RESEARCH

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

CAG expansion induces nucleolar stress in polyglutamine diseases

(2012) H. Tsoi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus

(2012) N. Lee et al.   RNA

CUGBP1 and MBNL1 preferentially bind to 3′ UTRs and facilitate mRNA decay

(2012) Akio Masuda et al.   Scientific Reports

C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes

(2012) Pietro Fratta et al.   Scientific Reports

Protein-RNA footprinting: an evolving tool

(2012) Dominique Fourmy et al.   Wiley Interdisciplinary Reviews-RNA

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Transient RNA-protein interactions in RNA folding

(2011) Martina Doetsch et al.   FEBS Journal

Perturbation of U2AF65/NXF1-mediated RNA nuclear export enhances RNA toxicity in polyQ diseases

(2011) Ho Tsoi et al.   HUMAN MOLECULAR GENETICS

Cellular toxicity of expanded RNA repeats: focus on RNA foci

(2011) Marzena Wojciechowska et al.   HUMAN MOLECULAR GENETICS

Transgenic mice with SCA10 pentanucleotide repeats show motor phenotype and susceptibility to seizure: A toxic RNA gain-of-function model

(2011) Misti White et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

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

Misregulation of miR-1 processing is associated with heart defects in myotonic dystrophy

(2011) Frédérique Rau et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Expanded GGGGCC Hexanucleotide Repeat in Noncoding Region of C9ORF72 Causes Chromosome 9p-Linked FTD and ALS

(2011) Mariely DeJesus-Hernandez et al.   NEURON

A Hexanucleotide Repeat Expansion in C9ORF72 Is the Cause of Chromosome 9p21-Linked ALS-FTD

(2011) Alan E. Renton et al.   NEURON

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

(2011) Joseph D. Shih et al.   NUCLEIC ACIDS RESEARCH

New function for the RNA helicase p68/DDX5 as a modifier of MBNL1 activity on expanded CUG repeats

(2011) François-Xavier Laurent et al.   NUCLEIC ACIDS RESEARCH

CAG repeats mimic CUG repeats in the misregulation of alternative splicing

(2011) Agnieszka Mykowska et al.   NUCLEIC ACIDS RESEARCH

hnRNP A1 and hnRNP F Modulate the Alternative Splicing of Exon 11 of the Insulin Receptor Gene

(2011) Indrani Talukdar et al.   PLoS One

Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3’ UTR structures

(2011) Alex Michael Ward et al.   RNA Biology

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

Primary Central Nervous System Lymphoma

(2010) Elizabeth R. Gerstner et al.   ARCHIVES OF NEUROLOGY

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

(2010) Markus Hafner et al.   CELL

FRET Microscopy in 2010: The Legacy of Theodor Förster on the 100th Anniversary of his Birth

(2010) Yuansheng Sun et al.   CHEMPHYSCHEM

Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients

(2010) Chantal Sellier et al.   EMBO JOURNAL

Proximity ligation assays: a recent addition to the proteomics toolbox

(2010) Irene Weibrecht et al.   Expert Review of Proteomics

Structural Diversity of Triplet Repeat RNAs

(2010) Krzysztof Sobczak et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity

(2010) S.-H. Chan et al.   NUCLEIC ACIDS RESEARCH

Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression

(2010) Angela C. Miniard et al.   NUCLEIC ACIDS RESEARCH

RNase-assisted RNA chromatography

(2010) G. Michlewski et al.   RNA

Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52

(2010) Y. Soeno et al.   RNA

RNA Regulation in Neurologic Disease and Cancer

(2010) Robert B. Darnell   Cancer Research and Treatment

Inactivation of hnRNP K by Expanded Intronic AUUCU Repeat Induces Apoptosis Via Translocation of PKCδ to Mitochondria in Spinocerebellar Ataxia 10

(2010) Misti C. White et al.   PLoS Genetics

Expression of RNA CCUG Repeats Dysregulates Translation and Degradation of Proteins in Myotonic Dystrophy 2 Patients

(2009) Elizabeth Salisbury et al.   AMERICAN JOURNAL OF PATHOLOGY

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor

(2009) M. Dienstbier et al.   GENES & DEVELOPMENT

Quantitative Proteomics by Metabolic Labeling of Model Organisms

(2009) Joost W. Gouw et al.   MOLECULAR & CELLULAR PROTEOMICS

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

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

In vivo detection of RNA-binding protein interactions with cognate RNA sequences by fluorescence resonance energy transfer

(2009) M. Huranova et al.   RNA

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

Tethering of proteins to RNAs by bacteriophage proteins

(2008) Cecile Keryer-Bibens et al.   BIOLOGY OF THE CELL

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Mechanisms of RNA-mediated Disease

(2008) Jason R. O'Rourke et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Determinants of MicroRNA Processing Inhibition by the Developmentally Regulated RNA-binding Protein Lin28

(2008) Elena Piskounova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Visualizing protein-RNA interactions inside cells by fluorescence resonance energy transfer

(2008) M. Lorenz   RNA

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS