Getting to the bottom of lncRNA mechanism: structure–function relationships

Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19

(2021) Jiahao Ma et al.   JOURNAL OF VIROLOGY

Structural analyses of an RNA stability element interacting with poly(A)

(2021) Seyed-Fakhreddin Torabi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

iDRiP for the systematic discovery of proteins bound directly to noncoding RNA

(2021) Hsueh-Ping Chu et al.   Nature Protocols

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

(2021) Bei Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Elongation Factor-Tu switch I is a gate for aminoacyl-tRNA selection

(2020) Dylan Girodat et al.   JOURNAL OF MOLECULAR BIOLOGY

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

(2020) Justin C. Morse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing the structure and motion of the long noncoding RNA HOTAIR

(2020) Rachel Spokoini-Stern et al.   RNA

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

(2020) Doo Nam Kim et al.   Nature Communications

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

(2020) Alessandro Bonetti et al.   Nature Communications

Cryo-EM structure of SWI/SNF complex bound to a nucleosome

(2020) Yan Han et al.   NATURE

Evaluating DCA-based method performances for RNA contact prediction by a well-curated dataset

(2020) Fabrizio Pucci et al.   RNA

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

(2020) Kalli Kappel et al.   NATURE METHODS

Structural Diversity and Phylogenetic Distribution of Valyl tRNA-like Structures in Viruses

(2020) Madeline E. Sherlock et al.   RNA

Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation

(2020) Sebastian M Fica   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome

(2019) Chuangye Yan et al.   Cold Spring Harbor Perspectives in Biology

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex

(2019) Chris H. Hill et al.   MOLECULAR CELL

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?

(2019) Robert M. Glaeser   Annual Review of Biophysics

An NMR View of Protein Dynamics in Health and Disease

(2019) Ashok Sekhar et al.   Annual Review of Biophysics

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

(2019) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

How to benchmark RNA secondary structure prediction accuracy

(2019) David H. Mathews   METHODS

The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases

(2019) Terence T. L. Tang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The mechanism of splicing as told by group II introns: Ancestors of the spliceosome

(2019) Claire M. Smathers et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway

(2019) Tina Uroda et al.   MOLECULAR CELL

Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome

(2019) Yoshimasa Takizawa et al.   STRUCTURE

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Mechanistic insights into mRNA 3′-end processing

(2019) Ananthanarayanan Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

(2019) Kaiming Zhang et al.   Nature Communications

Dynamic Neutron Scattering by Biological Systems

(2018) Jeremy C. Smith et al.   Annual Review of Biophysics

The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process

(2018) Yaser Hashem et al.   Annual Review of Biophysics

New Insights into Ribosome Structure and Function

(2018) Amy Jobe et al.   Cold Spring Harbor Perspectives in Biology

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

(2018) Susmita Roy et al.   NUCLEIC ACIDS RESEARCH

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

Visualizing the secondary and tertiary architectural domains of lncRNA RepA

(2017) Fei Liu et al.   Nature Chemical Biology

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

(2017) Jason Yao et al.   NUCLEIC ACIDS RESEARCH

Modeling RNA secondary structure folding ensembles using SHAPE mapping data

(2017) Aleksandar Spasic et al.   NUCLEIC ACIDS RESEARCH

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

(2017) Zhen Tan et al.   NUCLEIC ACIDS RESEARCH

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

(2017) Susmita Roy et al.   PLoS Computational Biology

RNA folding with hard and soft constraints

(2016) Ronny Lorenz et al.   Algorithms for Molecular Biology

Group II Intron Self-Splicing

(2016) Anna Marie Pyle   Annual Review of Biophysics

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

(2016) Alexander Borodavka et al.   BIOPHYSICAL JOURNAL

Predicting RNA secondary structures from sequence and probing data

(2016) Ronny Lorenz et al.   METHODS

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

(2016) Zhihong Xue et al.   MOLECULAR CELL

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

(2016) Michael R Wasserman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNAlien – Unsupervised RNA family model construction

(2016) Florian Eggenhofer et al.   NUCLEIC ACIDS RESEARCH

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

(2016) Michael R Wasserman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

(2016) Emily J. Hawkes et al.   Cell Reports

Biostructural Science Inspired by Next-Generation X-Ray Sources

(2015) Sol M. Gruner et al.   Annual Review of Biophysics

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA

(2015) Chen Davidovich et al.   MOLECULAR CELL

Functional Dynamics within the Human Ribosome Regulate the Rate of Active Protein Synthesis

(2015) Angelica Ferguson et al.   MOLECULAR CELL

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

(2015) Ryan L. Hayes et al.   PHYSICAL REVIEW LETTERS

Twenty years of RNA crystallography

(2015) Eric Westhof   RNA

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches

(2014) Ryan L. Hayes et al.   BIOPHYSICAL JOURNAL

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

(2014) Thomas R. Cech et al.   CELL

Structure and Function of Steroid Receptor RNA Activator Protein, the Proposed Partner of SRA Noncoding RNA

(2014) David B. McKay et al.   JOURNAL OF MOLECULAR BIOLOGY

Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome

(2014) Simão Teixeira da Rocha et al.   MOLECULAR CELL

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

(2014) Jessica A Brown et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs

(2014) Fabiana Arieti et al.   NUCLEIC ACIDS RESEARCH

Steroid Receptor RNA Activator (SRA) Modification by the Human Pseudouridine Synthase 1 (hPus1p): RNA Binding, Activity, and Atomic Model

(2014) Tiphaine Huet et al.   PLoS One

Physiological roles of long noncoding RNAs: insight from knockout mice

(2014) Lingjie Li et al.   TRENDS IN CELL BIOLOGY

Structural Basis of the Translational Elongation Cycle

(2013) Rebecca M. Voorhees et al.   Annual Review of Biochemistry

Molecular Mechanisms of RNA Interference

(2013) Ross C. Wilson et al.   Annual Review of Biophysics

Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology

(2013) Robert P. Rambo et al.   Annual Review of Biophysics

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems

(2013) Paul D. Adams et al.   Annual Review of Biophysics

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

(2013) Irina V. Novikova et al.   JOURNAL OF MOLECULAR BIOLOGY

3S: Shotgun secondary structure determination of long non-coding RNAs

(2013) Irina V. Novikova et al.   METHODS

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila

(2013) Ibrahim Avsar Ilik et al.   MOLECULAR CELL

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

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

(2013) Yue Wan et al.   Nature Protocols

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

(2012) Alexander Serganov et al.   Annual Review of Biophysics

Paraspeckle nuclear bodies—useful uselessness?

(2012) Shinichi Nakagawa et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Computational studies of molecular machines: the ribosome

(2012) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

Alternative 3′-end processing of long noncoding RNA initiates construction of nuclear paraspeckles

(2012) Takao Naganuma et al.   EMBO JOURNAL

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

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

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch

(2012) Scott P. Hennelly et al.   NUCLEIC ACIDS RESEARCH

Effect of Focal Ischemia on Long Noncoding RNAs

(2012) Ashutosh Dharap et al.   STROKE

SAXS Studies of Ion–Nucleic Acid Interactions

(2011) Lois Pollack   Annual Review of Biophysics

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Structure and Dynamics of a Processive Brownian Motor: The Translating Ribosome

(2010) Joachim Frank et al.   Annual Review of Biochemistry

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Challenges and opportunities for new protein crystallization strategies in structure-based drug design

(2010) Jessica Lynn Grey et al.   Expert Opinion on Drug Discovery

Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA

(2010) H. Yao et al.   GENES & DEVELOPMENT

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

(2010) Colby D. Stoddard et al.   STRUCTURE

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Dax-1 and Steroid Receptor RNA Activator (SRA) Function as Transcriptional Coactivators for Steroidogenic Factor 1 in Steroidogenesis

(2009) B. Xu et al.   MOLECULAR AND CELLULAR BIOLOGY

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

(2009) Szymon Swiezewski et al.   NATURE

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Navigating the ribosome's metastable energy landscape

(2009) James B. Munro et al.   TRENDS IN BIOCHEMICAL SCIENCES

Riboswitches: Emerging Themes in RNA Structure and Function

(2008) Rebecca K. Montange et al.   Annual Review of Biophysics

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

(2008) Jeremy E. Wilusz et al.   CELL

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

The RNA coregulator SRA, its binding proteins and nuclear receptor signaling activity

(2008) Shane M. Colley et al.   IUBMB LIFE

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Structure of the SAM-II riboswitch bound to S-adenosylmethionine

(2008) Sunny D Gilbert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A NMR strategy to unambiguously distinguish nucleic acid hairpin and duplex conformations applied to a Xist RNA A-repeat

(2008) Malgorzata M. Duszczyk et al.   NUCLEIC ACIDS RESEARCH

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE