Epitranscriptomic technologies and analyses

SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein–RNA interactions with high accuracy

(2019) Ya Zhao et al.   NUCLEIC ACIDS RESEARCH

Methods to study RNA–protein interactions

(2019) Muthukumar Ramanathan et al.   NATURE METHODS

fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: Lessons from DROSHA

(2018) Baekgyu Kim et al.   METHODS

Advances in CLIP Technologies for Studies of Protein-RNA Interactions

(2018) Flora C.Y. Lee et al.   MOLECULAR CELL

Light-activated chemical probing of nucleobase solvent accessibility inside cells

(2018) Chao Feng et al.   Nature Chemical Biology

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

(2018) Jean-Denis Beaudoin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GoldCLIP: Gel-omitted Ligation-dependent CLIP

(2018) Jiaqi Gu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

COMRADES determines in vivo RNA structures and interactions

(2018) Omer Ziv et al.   NATURE METHODS

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity

(2018) Pan Li et al.   Cell Host & Microbe

Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches

(2018) Xingyang Qian et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

(2018) Sunny Y. Yang et al.   Nature Communications

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms

(2017) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

DO-RIP-seq to quantify RNA binding sites transcriptome-wide

(2017) Cindo O. Nicholson et al.   METHODS

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

(2017) Qing Dai et al.   NATURE METHODS

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein

(2017) Yoichiro Sugimoto et al.   Nature Protocols

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions

(2017) Fei Qi et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications

(2017) Danny Incarnato et al.   TRENDS IN BIOTECHNOLOGY

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

(2017) Meiling Piao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

Dawn of the in vivo RNA structurome and interactome

(2016) Chun Kit Kwok   BIOCHEMICAL SOCIETY TRANSACTIONS

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data

(2016) Ankeeta Shah et al.   BIOINFORMATICS

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

(2016) Aoife C. McMahon et al.   CELL

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

(2016) Jong Ghut Ashley Aw et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

(2016) Chun Kit Kwok et al.   NATURE METHODS

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

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

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

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues

(2016) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA

(2016) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

(2016) Nicolai Krogh et al.   NUCLEIC ACIDS RESEARCH

Bridging the gap between in vitro and in vivo RNA folding

(2016) Kathleen A. Leamy et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

(2016) J. U. Guo et al.   SCIENCE

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

(2016) Tri C. Nguyen et al.   Nature Communications

Targeted Detection of G-Quadruplexes in Cellular RNAs

(2015) Chun Kit Kwok et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

RNA structure: Merging chemistry and genomics for a holistic perspective

(2015) Miles Kubota et al.   BIOESSAYS

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

(2015) Federico Comoglio et al.   BMC BIOINFORMATICS

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai et al.   MOLECULAR CELL

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

(2015) Yoichiro Sugimoto et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

High-throughput determination of RNA structure by proximity ligation

(2015) Vijay Ramani et al.   NATURE BIOTECHNOLOGY

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

StarScan: a web server for scanning small RNA targets from degradome sequencing data

(2015) Shun Liu et al.   NUCLEIC ACIDS RESEARCH

A comprehensive comparison of general RNA–RNA interaction prediction methods

(2015) Daniel Lai et al.   NUCLEIC ACIDS RESEARCH

CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite

(2015) Manolis Maragkakis et al.   RNA

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

(2015) Cristian Del Campo et al.   PLoS Genetics

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

(2015) Kirk W Gaston et al.   RNA Biology

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

(2014) M. Sakurai et al.   GENOME RESEARCH

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

(2014) Ralph D. Hector et al.   NUCLEIC ACIDS RESEARCH

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

(2014) David Loughrey et al.   NUCLEIC ACIDS RESEARCH

sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

(2014) Atul Kakrana et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

(2014) N. F. Dupuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

RNA triplexes: from structural principles to biological and biotech applications

(2014) Gitali Devi et al.   Wiley Interdisciplinary Reviews-RNA

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

(2014) Beibei Chen et al.   GENOME BIOLOGY

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

The Long and Short of MicroRNA

(2013) Luke A. Yates et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

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

(2013) Yiliang Ding et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

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

(2013) Silvi Rouskin et al.   NATURE

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

(2013) Michael T Lovci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides

(2013) Yuan Zhou 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

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

(2012) Anne Wenzel et al.   BIOINFORMATICS

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

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

(2012) Dan Dominissini et al.   NATURE

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Accurate identification of human Alu and non-Alu RNA editing sites

(2012) Gokul Ramaswami et al.   NATURE METHODS

Protein–RNA interactions: new genomic technologies and perspectives

(2012) Julian König et al.   NATURE REVIEWS GENETICS

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

(2012) Leighton Folkes et al.   NUCLEIC ACIDS RESEARCH

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

(2011) Sonja Althammer et al.   BIOINFORMATICS

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals

(2011) Young Seok Ju et al.   NATURE GENETICS

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

(2011) Yun Zheng et al.   NUCLEIC ACIDS RESEARCH

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

(2011) W. J. Krzyzosiak et al.   NUCLEIC ACIDS RESEARCH

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect

(2010) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing

(2010) Bjorn-Erik Wulff et al.   NATURE REVIEWS GENETICS

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

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

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo

(2010) Elisabeth M. Mahen et al.   PLOS BIOLOGY

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

(2010) Qi Zheng et al.   PLoS Genetics

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

(2009) Adam Roth et al.   Annual Review of Biochemistry

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Expanding roles for metabolite-sensing regulatory RNAs

(2009) Michael D Dambach et al.   CURRENT OPINION IN MICROBIOLOGY

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY