Specificity and nonspecificity in RNA–protein interactions

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

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

(2014) Ngoc Tam L Tran et al.   Biology Direct

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures

(2014) Carmen M Livi et al.   BMC BIOINFORMATICS

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

(2014) Jan P. Erzberger et al.   CELL

Building Robust Transcriptomes with Master Splicing Factors

(2014) Mohini Jangi et al.   CELL

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

(2014) Thomas R. Cech et al.   CELL

piRNAs: from biogenesis to function

(2014) E.-M. Weick et al.   DEVELOPMENT

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

(2014) J. Li et al.   GENOME RESEARCH

A Conserved Three-nucleotide Core Motif Defines Musashi RNA Binding Specificity

(2014) N. Ruth Zearfoss et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and Mechanistic Insights into Poly(uridine) Tract Recognition by the hnRNP C RNA Recognition Motif

(2014) Zuzana Cieniková et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Angiogenin-Cleaved tRNA Halves Interact with Cytochrome c, Protecting Cells from Apoptosis during Osmotic Stress

(2014) M. Saikia et al.   MOLECULAR AND CELLULAR BIOLOGY

Principles and Properties of Eukaryotic mRNPs

(2014) Sarah F. Mitchell et al.   MOLECULAR CELL

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

(2014) Nicole Lambert et al.   MOLECULAR CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Structure of an Rrp6–RNA exosome complex bound to poly(A) RNA

(2014) Elizabeth V. Wasmuth et al.   NATURE

Structural basis for the assembly of the Sxl–Unr translation regulatory complex

(2014) Janosch Hennig et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

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

(2014) Jacob M Tome et al.   NATURE METHODS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

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

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

Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution

(2014) Eric J Montemayor et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A protein-RNA specificity code enables targeted activation of an endogenous human transcript

(2014) Zachary T Campbell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The organization of RNA contacts by PTB for regulation ofFASsplicing

(2014) Ian Mickleburgh et al.   NUCLEIC ACIDS RESEARCH

Molecular basis for the wide range of affinity found in Csr/Rsm protein–RNA recognition

(2014) Olivier Duss et al.   NUCLEIC ACIDS RESEARCH

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function

(2014) Areum Han et al.   PLoS Computational Biology

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Methods for comprehensive experimental identification of RNA-protein interactions

(2014) Colleen A McHugh et al.   GENOME BIOLOGY

New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization

(2014) Abdullah Ozer et al.   Molecular Therapy-Nucleic Acids

Regulation of splicing by SR proteins and SR protein-specific kinases

(2013) Zhihong Zhou et al.   CHROMOSOMA

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Engineering RNA-binding proteins for biology

(2013) Yu Chen et al.   FEBS Journal

Engineered proteins with Pumilio/fem-3mRNA binding factor scaffold to manipulate RNA metabolism

(2013) Yang Wang et al.   FEBS Journal

New Insights into Functional Roles of the Polypyrimidine Tract-Binding Protein

(2013) Maria Romanelli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Crystal Structures and RNA-binding Properties of the RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein L

(2013) Wenjuan Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

(2013) Guramrit Singh et al.   METHODS

ATP-Dependent roX RNA Remodeling by the Helicase maleless Enables Specific Association of MSL Proteins

(2013) Sylvain Maenner et al.   MOLECULAR CELL

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

(2013) Shi-Yan Ng et al.   MOLECULAR CELL

An in vivo control map for the eukaryotic mRNA translation machinery

(2013) H. Firczuk et al.   Molecular Systems Biology

Hidden specificity in an apparently nonspecific RNA-binding protein

(2013) Ulf-Peter Guenther et al.   NATURE

Crystal structures of the Lsm complex bound to the 3′ end sequence of U6 small nuclear RNA

(2013) Lijun Zhou et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

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

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

A general approach for discriminative de novo motif discovery from high-throughput data

(2013) Jan Grau et al.   NUCLEIC ACIDS RESEARCH

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

(2013) N. Liu et al.   RNA

N6-methyl-adenosine modification in messenger and long non-coding RNA

(2013) Tao Pan   TRENDS IN BIOCHEMICAL SCIENCES

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

(2013) Katarzyna Zaremba-Niedzwiedzka et al.   GENOME BIOLOGY

The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus

(2012) Guramrit Singh et al.   CELL

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

(2012) Alfredo Castello et al.   CELL

Atomistic modeling of protein–DNA interaction specificity: progress and applications

(2012) Limin Angela Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

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

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

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

A mechanistic overview of translation initiation in eukaryotes

(2012) Colin Echeverría Aitken et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global analysis of yeast mRNPs

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

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites

(2012) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Engineering RNA endonucleases with customized sequence specificities

(2012) Rajarshi Choudhury et al.   Nature Communications

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

Computational methods for prediction of protein–RNA interactions

(2011) Tomasz Puton et al.   JOURNAL OF STRUCTURAL BIOLOGY

Angiogenin-Induced tRNA Fragments Inhibit Translation Initiation

(2011) Pavel Ivanov et al.   MOLECULAR CELL

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy

(2011) Jameson R Bothe et al.   NATURE METHODS

In silico characterization and prediction of global protein–mRNA interactions in yeast

(2011) Vera Pancaldi et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide analysis of protein–RNA interactions using high-throughput sequencing

(2011) Miha Milek et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

RNA nucleotide methylation

(2011) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

Toward a Consensus View of Duplex RNA Flexibility

(2010) Ignacio Faustino et al.   BIOPHYSICAL JOURNAL

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

(2010) Markus Hafner et al.   CELL

SF1 and SF2 helicases: family matters

(2010) Margaret E Fairman-Williams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functional organization of the Sm core in the crystal structure of human U1 snRNP

(2010) Gert Weber et al.   EMBO JOURNAL

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

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

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

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

(2010) C. Lorenz et al.   NUCLEIC ACIDS RESEARCH

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

(2010) Rahul Siddharthan   PLoS One

RNA looping by PTB: Evidence using FRET and NMR spectroscopy for a role in splicing repression

(2010) R. Lamichhane et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The REM phase of gene regulation

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

RNA decay modulates gene expression and controls its fidelity

(2010) Shubhendu Ghosh et al.   Wiley Interdisciplinary Reviews-RNA

The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect

(2009) Travis Thomson et al.   Annual Review of Cell and Developmental Biology

Topology and Regulation of the Human eIF4A/4G/4H Helicase Complex in Translation Initiation

(2009) Assen Marintchev et al.   CELL

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

RNA processing and its regulation: global insights into biological networks

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

Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu

(2009) Xabier Agirrezabala et al.   QUARTERLY REVIEWS OF BIOPHYSICS

The DAZL and PABP families: RNA-binding proteins with interrelated roles in translational control in oocytes

(2009) Matthew Brook et al.   REPRODUCTION

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

RNA recognition motifs: boring? Not quite

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

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

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

(2008) Donny D. Licatalosi et al.   NATURE

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

Extracting sequence features to predict protein–DNA interactions: a comparative study

(2008) Qing Zhou et al.   NUCLEIC ACIDS RESEARCH

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA