The molecular structure of long non-coding RNAs: emerging patterns and functional implications

Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations

(2020) Toru Niina et al.   Journal of Chemical Theory and Computation

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

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

(2020) Phillip J. Tomezsko et al.   NATURE

U1 snRNP regulates chromatin retention of noncoding RNAs

(2020) Yafei Yin et al.   NATURE

Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques

(2020) Tina Uroda et al.   Nature Protocols

The Sox2 transcription factor binds RNA

(2020) Zachariah E. Holmes et al.   Nature Communications

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

(2020) Kalli Kappel et al.   NATURE METHODS

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds

(2020) Andrew Martin Watkins et al.   STRUCTURE

Visualizing group II intron dynamics between the first and second steps of splicing

(2020) Jacopo Manigrasso et al.   Nature Communications

The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability

(2019) Nicole Bettin et al.   Cells

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization

(2019) Joana Carlevaro-Fita et al.   MOLECULAR CELL

Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

(2019) Rafael C.A. Tavares et al.   JOURNAL OF MOLECULAR BIOLOGY

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

(2019) Kaia Mattioli et al.   GENOME RESEARCH

RNA dynamics by NMR

(2019) Maja Marušič et al.   CHEMBIOCHEM

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

(2019) Lisa Marie Simon et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Steven Busan et al.   BIOCHEMISTRY

Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA

(2019) Daniel B. Haack et al.   CELL

Developmental dynamics of lncRNAs across mammalian organs and species

(2019) Ioannis Sarropoulos et al.   NATURE

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

(2019) Andrew M. Smith et al.   PLoS One

Microfluidic protein isolation and sample preparation for high-resolution cryo-EM

(2019) Claudio Schmidli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images

(2019) Bhaskar Dasgupta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

(2019) Tina Uroda et al.   MOLECULAR CELL

Computational design of three-dimensional RNA structure and function

(2019) Joseph D. Yesselman et al.   Nature Nanotechnology

RNA 3D structure prediction guided by independent folding of homologous sequences

(2019) Marcin Magnus et al.   BMC BIOINFORMATICS

Secondary Structural Model of Human MALAT1 Reveals Multiple Structure–Function Relationships

(2019) Phillip J. McCown et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

(2019) Jaswinder Singh et al.   Nature Communications

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

(2019) Kaiming Zhang et al.   Nature Communications

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures

(2018) Hosna Jabbari et al.   BIOINFORMATICS

A simple and robust procedure for preparing graphene-oxide cryo-EM grids

(2018) Eugene Palovcak et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

(2018) Yoav Lubelsky et al.   NATURE

Small molecules get the message

(2018) Justin Petrone et al.   NATURE BIOTECHNOLOGY

Functional classification of long non-coding RNAs by k-mer content

(2018) Jessime M. Kirk et al.   NATURE GENETICS

Structural characterization of maternally expressed gene 3 RNA reveals conserved motifs and potential sites of interaction with polycomb repressive complex 2

(2018) Chringma Sherpa et al.   NUCLEIC ACIDS RESEARCH

A novel phase-shift-based amplitude detector for a high-speed atomic force microscope

(2018) Atsushi Miyagi et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Selecting New RNA Crystal Contacts

(2018) Anastassia Gomez et al.   STRUCTURE

New tools for the analysis and validation of cryo-EM maps and atomic models

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Detection of long non–coding RNA homology, a comparative study on alignment and alignment–free metrics

(2018) Teresa M. R. Noviello et al.   BMC BIOINFORMATICS

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Extracting information from RNA SHAPE data: Kalman filtering approach

(2018) Sana Vaziri et al.   PLoS One

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

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

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods

(2017) Trushar R. Patel et al.   METHODS

Structure determination of group II introns

(2017) Timothy Wiryaman et al.   METHODS

Targeting of Polycomb Repressive Complex 2 to RNA by Short Repeats of Consecutive Guanines

(2017) Xueyin Wang et al.   MOLECULAR CELL

Visualizing the secondary and tertiary architectural domains of lncRNA RepA

(2017) Fei Liu et al.   Nature Chemical Biology

RNA modifications and structures cooperate to guide RNA–protein interactions

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

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

(2017) Nian Liu et al.   NUCLEIC ACIDS RESEARCH

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

RNA structure inference through chemical mapping after accidental or intentional mutations

(2017) Clarence Y. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization of RNA structure models within the Integrative Genomics Viewer

(2017) Steven Busan et al.   RNA

A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM

(2017) Xiangsong Feng et al.   STRUCTURE

Transcriptomics technologies

(2017) Rohan Lowe et al.   PLoS Computational Biology

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

(2017) Michael F. Sloma et al.   PLoS Computational Biology

Group II Intron Self-Splicing

(2016) Anna Marie Pyle   Annual Review of Biophysics

The ins and outs of lncRNA structure: How, why and what comes next?

(2016) Amanda J. Blythe et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome

(2016) Kaori Kashi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2016) Zhipeng Lu et al.   CELL

Small-angle scattering and 3D structure interpretation

(2016) Jill Trewhella   CURRENT OPINION IN STRUCTURAL BIOLOGY

Small Molecule-Based Pattern Recognition To Classify RNA Structure

(2016) Christopher S. Eubanks et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures

(2016) Nathan Pirakitikulr et al.   MOLECULAR CELL

Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA

(2016) Carika Weldon et al.   Nature Chemical Biology

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing

(2016) Shanshan Hu 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

Using in-cell SHAPE-Seq and simulations to probe structure–function design principles of RNA transcriptional regulators

(2016) Melissa K. Takahashi et al.   RNA

Comparison of SHAPE reagents for mapping RNA structures inside living cells

(2016) Byron Lee et al.   RNA

Cotranscriptional folding of a riboswitch at nucleotide resolution

(2016) Kyle E Watters et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing

(2016) Shanshan Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

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

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

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

(2015) Chen Davidovich et al.   MOLECULAR CELL

Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation

(2015) Valentina Ahl 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

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

(2015) Nian Liu et al.   NATURE

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

(2015) Chen Zhao et al.   Nature Chemical Biology

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Telomeric repeat-containing RNA/G-quadruplex-forming sequences cause genome-wide alteration of gene expression in human cancer cells in vivo

(2015) Kyotaro Hirashima et al.   NUCLEIC ACIDS RESEARCH

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Functionally conserved architecture of hepatitis C virus RNA genomes

(2015) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting RNA 3D structure using a coarse-grain helix-centered model

(2015) Peter Kerpedjiev et al.   RNA

The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs

(2015) Eugene Z. Kim et al.   RNA

Structure of the HIV-1 RNA packaging signal

(2015) S. C. Keane et al.   SCIENCE

SHAPE analysis of the RNA secondary structure of the Mouse Hepatitis Virus 5’ untranslated region and N-terminal nsp1 coding sequences

(2015) Dong Yang et al.   VIROLOGY

De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

(2015) Jinwen Yu et al.   Nature Communications

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

(2014) B. Zhang et al.   MOLECULAR AND CELLULAR BIOLOGY

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

Looking at LncRNAs with the Ribozyme Toolkit

(2014) Anna Marie Pyle   MOLECULAR CELL

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

(2014) Nadya Dimitrova et al.   MOLECULAR CELL

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

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

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

A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy

(2014) Ana García-Sacristán et al.   NUCLEIC ACIDS RESEARCH

LncRBase: An Enriched Resource for lncRNA Information

(2014) Sohini Chakraborty et al.   PLoS One

AntisenseCOOLAIRmediates the coordinated switching of chromatin states atFLCduring vernalization

(2014) Tibor Csorba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vitro characterization of the splicing efficiency and fidelity of the RmInt1 group II intron as a means of controlling the dispersion of its host mobile element

(2014) Isabel Chillón et al.   RNA

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

(2014) G. M. Rice et al.   RNA

Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

(2014) Sofia Quinodoz et al.   TRENDS IN CELL BIOLOGY

The four dimensions of noncoding RNA conservation

(2014) Sven Diederichs   TRENDS IN GENETICS

Conserved sequence-specific lincRNA–steroid receptor interactions drive transcriptional repression and direct cell fate

(2014) William H. Hudson et al.   Nature Communications

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

(2014) Rajika Arora et al.   Nature Communications

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Cryo-EM enters a new era

(2014) Werner Kühlbrandt   eLife

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

(2013) Marco Marcia et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Binding Interactions between Long Noncoding RNA HOTAIR and PRC2 Proteins

(2013) Liang Wu et al.   BIOCHEMISTRY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

Describing intrinsically disordered proteins at atomic resolution by NMR

(2013) Malene Ringkjøbing Jensen et al.   CURRENT OPINION IN STRUCTURAL 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

Reciprocal Regulation of HIF-1α and LincRNA-p21 Modulates the Warburg Effect

(2013) Fan Yang et al.   MOLECULAR CELL

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

(2013) Yiliang Ding et al.   NATURE

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Promiscuous RNA binding by Polycomb repressive complex 2

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

Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence

(2013) Bettina Balk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells

(2013) Jakub Minks et al.   Epigenetics & Chromatin

Structure of the full-length HCV IRES in solution

(2013) Julien Pérard et al.   Nature Communications

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

(2013) Lingjie Li et al.   Cell Reports

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

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

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

Visualizing Group II Intron Catalysis through the Stages of Splicing

(2012) Marco Marcia 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 determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

(2012) H. Tani et al.   GENOME RESEARCH

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

Discrete RNA Libraries from Pseudo-Torsional Space

(2012) Elisabeth Humphris-Narayanan et al.   JOURNAL OF MOLECULAR BIOLOGY

Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity

(2012) Kady-Ann Steen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda 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

QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

(2012) F. Karabiber et al.   RNA

Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch

(2012) K. L. Frieda et al.   SCIENCE

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

(2012) Minh-Hieu Trinh et al.   STRUCTURE

Exploring RNA Structural Codes with SHAPE Chemistry

(2011) Kevin M. Weeks et al.   ACCOUNTS OF CHEMICAL RESEARCH

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

A folding algorithm for extended RNA secondary structures

(2011) C. H. zu Siederdissen et al.   BIOINFORMATICS

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

(2011) Zasha Weinberg et al.   BMC BIOINFORMATICS

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Origin and evolution of SINEs in eukaryotic genomes

(2011) D A Kramerov et al.   HEREDITY

Imaging of nucleic acids with atomic force microscopy

(2011) Yuri L. Lyubchenko et al.   METHODS

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of pri-miRNA tertiary structure in miR-17~92 miRNA biogenesis

(2011) Steven G Chaulk et al.   RNA Biology

The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization

(2011) M. M. Duszczyk et al.   RNA

A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

(2011) W. Kladwang et al.   RNA

Correlating SHAPE signatures with three-dimensional RNA structures

(2011) E. Bindewald et al.   RNA

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Expression and Function of a Large Non-coding RNA Gene XIST in Human Cancer

(2011) Sarah M. Weakley et al.   WORLD JOURNAL OF SURGERY

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

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

(2010) Maite Huarte et al.   CELL

The tertiary structure of group II introns: implications for biological function and evolution

(2010) Anna Marie Pyle   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex

(2010) Gavin W. Collie et al.   NUCLEIC ACIDS RESEARCH

Nondenaturing Purification of Co-Transcriptionally Folded RNA Avoids Common Folding Heterogeneity

(2010) Miguel J. B. Pereira et al.   PLoS One

Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography

(2010) L. E. Easton et al.   RNA

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

(2010) R. M. Mitton-Fry et al.   SCIENCE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Structural analysis provides insights into the modular organization of picornavirus IRES

(2010) Noemí Fernández et al.   VIROLOGY

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

InvAluable junk: The cellular impact and function of Alu and B2 RNAs

(2009) Ryan D. Walters et al.   IUBMB LIFE

Analysis of Four-Way Junctions in RNA Structures

(2009) Christian Laing et al.   JOURNAL OF MOLECULAR BIOLOGY

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

(2009) Zasha Weinberg et al.   NATURE

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

In vitro characterization of a miR-122-sensitive double-helical switch element in the 5′ region of hepatitis C virus RNA

(2009) Rosa Díaz-Toledano et al.   NUCLEIC ACIDS RESEARCH

In vivo expression and purification of aptamer-tagged small RNA regulators

(2009) Nelly Said et al.   NUCLEIC ACIDS RESEARCH

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

G-Quadruplex Formation by Human Telomeric Repeats-Containing RNA in Na+Solution

(2008) Yan Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2008) Marc Parisien et al.   NATURE

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinctive structures between chimpanzee and humanin a brain noncoding RNA

(2008) A. Beniaminov et al.   RNA

ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

(2008) S. M. Vasa et al.   RNA

Crystal Structure of a Self-Spliced Group II Intron

(2008) N. Toor et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

A Kinetic Intermediate that Regulates Proper Folding of a Group II Intron RNA

(2007) Christina Waldsich et al.   JOURNAL OF MOLECULAR BIOLOGY