Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

A protein assembly mediates Xist localization and gene silencing

(2020) Amy Pandya-Jones et al.   NATURE

Methods to study RNA–protein interactions

(2019) Muthukumar Ramanathan et al.   NATURE METHODS

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

(2019) David Colognori et al.   MOLECULAR CELL

N-terminal sequences in matrin 3 mediate phase separation into droplet-like structures that recruit TDP43 variants lacking RNA binding elements

(2019) M. Carolina Gallego-Iradi et al.   LABORATORY INVESTIGATION

Phase separation drives X-chromosome inactivation: a hypothesis

(2019) Andrea Cerase et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

(2019) Steven Busan et al.   BIOCHEMISTRY

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

(2019) Rui Xiao et al.   CELL

Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation

(2019) Tatyana B. Nesterova et al.   Nature Communications

Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells

(2019) Arnab Sengupta et al.   PLOS BIOLOGY

RNA base-pairing complexity in living cells visualized by correlated chemical probing

(2019) Anthony M. Mustoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression

(2018) Cindy Meyer et al.   MOLECULAR CELL

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

In vitro reconstitution and analysis of eukaryotic RNase P RNPs

(2018) Anna Perederina et al.   NUCLEIC ACIDS RESEARCH

The Role of Xist in X-Chromosome Dosage Compensation

(2018) Anna Sahakyan et al.   TRENDS IN CELL BIOLOGY

TIA-1 Self-Multimerization, Phase Separation, and Recruitment into Stress Granules Are Dynamically Regulated by Zn 2+

(2018) Joseph B. Rayman et al.   Cell Reports

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

(2018) Jan Attig et al.   CELL

Protein-RNA Interactions: Structural Characteristics and Hotspot Amino Acids

(2018) Dennis M. Krüger et al.   RNA

The Future of Cross-Linking and Immunoprecipitation (CLIP)

(2018) Jernej Ule et al.   Cold Spring Harbor Perspectives in Biology

Cryo-EM Structure of the Human Ribonuclease P Holoenzyme

(2018) Jian Wu et al.   CELL

A Short Tandem Repeat-Enriched RNA Assembles a Nuclear Compartment to Control Alternative Splicing and Promote Cell Survival

(2018) Karen Yap et al.   MOLECULAR CELL

The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory

(2017) Rebeca Ridings-Figueroa et al.   GENES & DEVELOPMENT

Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing

(2017) Yuri Uemura et al.   GENES TO CELLS

Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins

(2017) Aitor Garzia et al.   METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1)

(2017) Hongjae Sunwoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

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

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

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

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

Control of Chromosomal Localization of Xist by hnRNP U Family Molecules

(2016) Takehisa Sakaguchi et al.   DEVELOPMENTAL CELL

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

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

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

A U1 snRNP–specific assembly pathway reveals the SMN complex as a versatile hub for RNP exchange

(2016) Byung Ran So et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A U1 snRNP–specific assembly pathway reveals the SMN complex as a versatile hub for RNP exchange

(2016) Byung Ran So et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

(2015) Marco Y. Hein et al.   CELL

Photo-lysine captures proteins that bind lysine post-translational modifications

(2015) Tangpo Yang et al.   Nature Chemical Biology

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

(2015) Inessa De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture

(2015) Nozomi Sugimoto et al.   NUCLEIC ACIDS RESEARCH

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

(2015) Inessa De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing

(2015) Benoit Moindrot et al.   Cell Reports

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5′ splice site recognition

(2015) Yasushi Kondo et al.   eLife

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

Structures of the human and Drosophila 80S ribosome

(2013) Andreas M. Anger et al.   NATURE

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

(2013) Mallory A Freeberg et al.   GENOME BIOLOGY

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing

(2012) Frank Rigo et al.   Nature Chemical Biology

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Aliphatic Diazirines as Photoaffinity Probes for Proteins: Recent Developments

(2011) Joydip Das   CHEMICAL REVIEWS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

(2010) E. Kuhn-Holsken et al.   NUCLEIC ACIDS RESEARCH

Of proteins and RNA: The RNase P/MRP family

(2010) O. Esakova et al.   RNA

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Chemical cross-linking with NHS esters: a systematic study on amino acid reactivities

(2009) Stefanie Mädler et al.   JOURNAL OF MASS SPECTROMETRY

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution

(2009) Daniel A. Pomeranz Krummel et al.   NATURE

The SR protein family of splicing factors: master regulators of gene expression

(2008) Jennifer C. Long et al.   BIOCHEMICAL JOURNAL

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT