RNA modifications and structures cooperate to guide RNA–protein interactions

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

(2016) Zhipeng Lu et al.   CELL

Posttranscriptional m 6 A Editing of HIV-1 mRNAs Enhances Viral Gene Expression

(2016) Edward M. Kennedy et al.   Cell Host & Microbe

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export

(2016) Michaela Müller-McNicoll et al.   GENES & DEVELOPMENT

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation

(2016) J. Matthew Taliaferro et al.   MOLECULAR 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

m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination

(2016) Irmgard U. Haussmann et al.   NATURE

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

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

(2016) Xiaoyu Li et al.   Nature Chemical Biology

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

pVHL suppresses kinase activity of Akt in a proline-hydroxylation-dependent manner

(2016) J. Guo et al.   SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure

(2016) Jinwei Zhang et al.   TRENDS IN BIOCHEMICAL SCIENCES

YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex

(2016) Hao Du et al.   Nature Communications

Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi

(2016) Kazimierz T. Tycowski et al.   Cell Reports

Regulatory effects of cotranscriptional RNA structure formation and transitions

(2016) Sheng-Rui Liu et al.   Wiley Interdisciplinary Reviews-RNA

N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression

(2016) Nagaraja Tirumuru et al.   eLife

NSun2 delays replicative senescence by repressing p27 (KIP1) translation and elevating CDK1 translation

(2015) Hao Tang et al.   Aging-US

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events

(2015) Claudio R. Alarcón et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency

(2015) Tong Chen et al.   Cell Stem Cell

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

NSun2 Promotes Cell Growth via Elevating Cyclin-Dependent Kinase 1 Translation

(2015) Junyue Xing et al.   MOLECULAR AND CELLULAR BIOLOGY

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón et al.   NATURE

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

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

Transcriptome-wide dynamics of RNA pseudouridylation

(2015) John Karijolich et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

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

(2014) Schraga Schwartz et al.   CELL

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

(2014) Thomas R. Cech et al.   CELL

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

(2014) Xu Zhao et al.   CELL RESEARCH

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Tet-Mediated Formation of 5-Hydroxymethylcytosine in RNA

(2014) Lijuan Fu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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 G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

(2014) Andrew L. Wolfe et al.   NATURE

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

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

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

The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity

(2014) Jacki E. Heraud-Farlow et al.   TRENDS IN NEUROSCIENCES

MOV10 and FMRP Regulate AGO2 Association with MicroRNA Recognition Elements

(2014) Phillip J. Kenny et al.   Cell Reports

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

(2014) Schraga Schwartz et al.   Cell Reports

The RNAissance family: SR proteins as multifaceted regulators of gene expression

(2014) Jonathan M. Howard et al.   Wiley Interdisciplinary Reviews-RNA

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

Identification of Wilms' Tumor 1-associating Protein Complex and Its Role in Alternative Splicing and the Cell Cycle

(2013) Keiko Horiuchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2013) Yiliang Ding et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

(2013) Silvi Rouskin et al.   NATURE

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

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

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

(2013) N. Liu et al.   RNA

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

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

(2012) Guramrit Singh et al.   CELL

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

(2012) Kate D. Meyer et al.   CELL

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

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

5'-UTR RNA G-quadruplexes: translation regulation and targeting

(2012) A. Bugaut et al.   NUCLEIC ACIDS RESEARCH

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

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

Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN  noncoding RNAs

(2012) J. A. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

hnRNP C Tetramer Measures RNA Length to Classify RNA Polymerase II Transcripts for Export

(2012) A. McCloskey et al.   SCIENCE

RNA Methylation by the MIS Complex Regulates a Cell Fate Decision in Yeast

(2012) Sudeep D. Agarwala et al.   PLoS Genetics

G-quadruplexes in RNA biology

(2012) Stefania Millevoi et al.   Wiley Interdisciplinary Reviews-RNA

RNA polymerase II kinetics inpolopolyadenylation signal selection

(2011) Pedro A B Pinto et al.   EMBO JOURNAL

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

New insights into RNA secondary structure in the alternative splicing of pre-mRNAs

(2011) Yongfeng Jin et al.   RNA Biology

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

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

(2010) Markus Hafner et al.   CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Deciphering the splicing code

(2010) Yoseph Barash 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

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

APOBEC-1-mediated RNA editing

(2010) Valerie Blanc et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

Regulation of SR protein phosphorylation and alternative splicing by modulating kinetic interactions of SRPK1 with molecular chaperones

(2009) X.-Y. Zhong et al.   GENES & DEVELOPMENT

SR Proteins in Vertical Integration of Gene Expression from Transcription to RNA Processing to Translation

(2009) Xiang-Yang Zhong et al.   MOLECULAR CELL

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

MEN  /  nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

(2008) H. Sunwoo et al.   GENOME RESEARCH

“Nought May Endure but Mutability”: Spliceosome Dynamics and the Regulation of Splicing

(2008) Duncan J. Smith et al.   MOLECULAR CELL

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL