RNA

Article	Citations
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	148
Novel trinucleotide mRNA capping reagents: improved synthetic route and efficient cotranscriptional incorporation in mRNA	129
Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor	111
Motifs in SARS-CoV-2 evolution	81
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	66
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	49
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	45
Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (	43
Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts	39
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	35
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	34
Simultaneous detection of the AAV genomes and their transcripts in situ at the single-cell level	32
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	31
Molecular basis for GIGYF–TNRC6 complex assembly	31
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	30
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	29
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	29
Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2	29
Corrigendum: Pharmacologically stabilizing RNA G-quadruplexes in coronavirus genome reduces infectivity	28
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	28
Far from home: the role of glial mRNA localization in synaptic plasticity	28
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	27
PANTHER Score: Protein-Affinity for Nucleic Target-binding, Hybridization, and Energy Regression	27
Exploring the targeting spectrum of rocaglates among eIF4A homologs	26
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	25

Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection	25
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	25
mRNA COVID-19 vaccines: science versus misinformation	24
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor	23
The m6A-binding protein YTHDF3 modulates the cardiac response to stress	23
Reconstitution of antiviral Dicer activity in vitro reveals distinct contributions of RDE-4 dsRNA-binding motifs	23
Nuclear RNA-binding proteins meet cytoplasmic viruses	22
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	22
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	22
A novel reporter for helicase activity in translation uncovers DDX3X interactions	22
Diversity and modularity of tyrosine-accepting tRNA-like structures	21
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	21
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	21
Target-site Dynamics Explain a Large Share of Apparent MicroRNA Differential Expression	21
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	21
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	20
Progress and challenges in profiling protein–RNA and protein-associated RNA–RNA interactions	20
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	20
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	20
Human vault RNAs exhibit diverse expression patterns and inter-locus compensation	20
Adenosine deaminases that act on RNA, then and now	20
Terminal loop sequences in viral double-stranded RNAs modulate RIG-I signaling	20
Novel ADAR2 variants in children with seizures, intellectual disability, and motor delay have reduced RNA editing	19
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	19
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	19
Decoding Argonaute specificity: insights from C. elegans and beyond	18
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	18
Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting	18
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	17
PACT suppresses PKR activation through dsRNA binding and dimerization, and is a therapeutic target for triple-negative breast cancer	17
Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNAIle(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA	17
Seven wonders of RNA modification biology	16
EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides	16
Codon bias shapes bacterial small RNA binding sites within protein-coding sequences	16
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	16
clipplotr —a comparative visualization and analysis tool for CLIP data	16
An incredible life in science: Joseph G. Gall (1928–2024)	16
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	16
The pseudotorsional space of RNA	15
SMDesigner: a program to design sequence mutations to assess RNA structure	15
Desthiobiotin (DTB)–modified and TAMRA-modified 2″OMeNAD + are RNA 2′-phosphotransferase (Tpt1) poisons that enable affinity-tagging and fluorescence	15
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells	15
Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery	14
Localization of RNAs to the Mitochondria – Mechanisms and Functions	14
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	14
Boosting the toolbox for live imaging of translation	14
Corrigendum: No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV, and MLV viral RNA	14
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	14
The codon context provides cis -acting immune evasion for the human papilloma virus (HPV) E6	14
Translation elongation inhibitors stabilize select short-lived transcripts	14

RNA modifications: an overview of select web-based tools	14
Solution Structure Determination and Biophysical Studies of 7SK RNP and 7SL SRP RNAs	13
miRNA regulation in brain tissue space: the 3′UTR perspective	13
RK-33 inhibits the OC43 Coronavirus and induces stress granules via DDX3X-independent mechanisms	13
Implications for OLE RNA as a natural integral membrane RNA	13
Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7	13
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53-mediated tumor suppression	13
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	13
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	13
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	13
Dual Role of 3′ UTR Length in Modulating Translation Termination Efficiency	13
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	13
4MRNA: a new approach for nucleic acid molecular replacement using models with diverse parameter patterns	12
Editing-independent effects of Drosophila Adar on heterochromatin silencing	12
Reconfigured immunity in Adar heterozygous and Adar Mavs Eif2ak2 (PKR) triple mutant mice	12
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	12
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	12
OpenASO: RNA Rescue—designing splice-modulating antisense oligonucleotides through community science	12
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	12
Walter Keller (1938–2023): a tribute from his mentees	12
Ancestral intronic splicing regulatory elements in the SCNα gene family	12
A continuum-based reaction-diffusion model for spread of gene silencing in chromosomal inactivation	12
C. elegans FBF-1 and FBF-2 C-terminal intrinsically-disordered regions differentially regulate RNA-binding affinity	11
The importance of m 6 A topology in chicken embryo mRNA: a precise mapping of m 6 A at the conserv	11
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	11
Computational design and experimental verification of pseudoknotted ribozymes	11
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	11
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	11
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	11
The daunting task of modifying ribosomal RNA	11
Conformational dynamics of the hepatitis C virus 3′X RNA	11
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	11
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	11
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	11
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	11
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	11
ZYS-1 is not an ADAR1 inhibitor	11
DNMT1 inhibition by pUG-fold quadruplex RNA	10
Molecular basis of human polyA polymerase recruitment by mPSF	10
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	10
RNA G-quadruplex structure targeting and imaging: recent advances and future directions	10
Global analysis by LC-MS/MS of N6 -methyladenosine and inosine in mRNA reveal complex incidence	10
Chemical manipulation of m1A mediates its detection in human tRNA	10
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	10
Understanding the redundant functions of the m6A-binding YTHDF proteins	10
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	10
ac4C: a fragile modification with stabilizing functions in RNA metabolism	10
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	9
The unfolding landscape of RNA and disease	9
RNA gain-of-function mechanisms in short tandem repeat diseases	9
Targeting splicing factors for cancer therapy	9
Onconeural antigen NOVA1 dysregulates RNA alternative splicing in breast cancer	9
The role of nonsense-mediated mRNA decay in restricting long noncoding RNA expression has been conserved in RNAi-capable budding yeast	9
Promiscuous RNA editing in lncRNA roX1 is generally non-adaptive	9
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	9
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	9
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	9
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	9
Study of the RNA splicing kinetics via in vivo 5-EU labeling	9
KRGG1 function in RNA editing inTrypanosoma brucei	9
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	9
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	8
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	8
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	8
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	8
RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins	8
Splice site diversity and abundance of noncanonical introns in diplonemids (Diplonemea, Euglenozoa)	8
Comparative analysis of the m6A epitranscriptome in HeLa-expressed HPV18 early transcripts reveals its potential impact on splicing	8
Cancer-associated synonymous mutations reveal stress signal-dependent mRNA folding that selectively modulates protein function.	8
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	8
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	8
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	8
Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops	8
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	8
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor in Saccharomyces cerevisiae	8
How tailored Ribo-seq methods probe unique translation events	8
Examining SRP pathway function in mRNA localization to the endoplasmic reticulum	7
Crystal structures of free-state tRNALeu reveal conformational flexibility of type-II tRNAs	7
R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes	7
m6A-ELISA, a simple method for quantifying N6 -methyladenosine from mRNA populations	7

Interdomain assembly between the fungal tRNA ligase adenylyltransferase and kinase domain	7
AUA codon decoding by preferential use of tRNA Ile (UAU) in Lactobacillus casei	7
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast	7
A comparison of Dictyostelium discoideum 3′-5′ RNA polymerases reveals a conserved tRNA His guanylyltr	7
Blocky proline/glutamine patterns in the SFPQ intrinsically disordered region dictate paraspeckle formation as a distinct membraneless organelle	7
The life and times of a tRNA	7
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome	7
Is there a localized role for translational quality control?	7
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells	7
Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members	7
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line	7
Tral tunes condensate phase behavior and mRNA partitioning to regulate P-body homeostasis during Drosophila melanogaster nurse cells	7
Theje ne sais quoiof 5-methylcytosine in messenger RNA	7
Tribute to Yoshiro Shimura (1932–2023)	7
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures	7
P Can PIE: A group I intron platform for efficient circRNA synthesis at ambient temperatures	7
Robo-Therm, a pipeline to RNA Thermometer discovery and validation	6
First full-genome alignment representative for the genus Pestivirus	6
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	6
Past studies suggest potential therapies for newly discovered retinitis pigmentosa mutations in U6 and U4 snRNAs	6
Human T-cell leukemia virus type 1 uses a specific tRNAProisodecoder to prime reverse transcription	6
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging	6
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data	6
Recollections: Yasuhiro Furuichi (1940–2022)	6
Quantification of tRNA m1A modification by templated-ligation qPCR	6
Nuclear basket subunits Nup211 and Rsm1 influence RNA 3′-processing and transcription termination in fission yeast	6
Proteins that recognize unique features of U7 snRNA and may substitute for Gemin5 in the assembly of U7-specific Sm ring	6
40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion	6
Context-dependent phosphorylation of CSDE1 drives interactions with ribosomes	6
System-level measurement, modeling, and manipulation of RNA	6
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing	6
On the origin of life: an RNA-focused synthesis and narrative	6
2′-O-methylation (Nm) in RNA: progress, challenges, and future directions	6
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	6
Rapid disassembly and Piwi-independent reassembly of Drosophila piRNA cluster heterochromatin following acute heat shock	6
Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes	6
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding	6
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq	6
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging	6
Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development	6
Alu RNA pseudoknot alterations influence SRP9/SRP14 association	6
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	6
Detection of stress-dependent m 5 C rRNA dynamics in Escherichia coli using m	6
Fungi of the order Mucorales express a “sealing-only” tRNA ligase	5
Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling	5
A general and biomedical perspective of viral quasispecies	5
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	5
New mechanistic insights into prespliceosome formation—roles of DEAD-box proteins Prp5 and Sub2	5
Conserved protein Seb1 that interacts with RNA polymerase II and RNA is an antipausing transcription elongation factor	5
Corrigendum: Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins	5
MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing	5
M6A methylation inhibits recruitment of the Dand5 3’UTR to the left-right determinant Bicc1	5
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance	5
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection	5
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA	5
In vivo structure probing of RNA in Archaea : novel insights into the ribosome structure of Methanosarcina acetivorans	5
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	5
ykkC -I riboswitch aptamer domain requires an interplay between metal triad and cationic ligand: insights into metal ion–induced allostery from molecular dynamics simulation	5
Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation	5
A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions	5
Dissecting the stress granule RNA world: dynamics, strategies, and data	5
Integrated NMR and MD structure and dynamics of the stem–loop-II motif (s2m) from the Omicron variant of SARS-CoV-2	5
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	5
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	5
Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts	5
Cytosolic and ER-associated ribosomes share rRNA 2′-O-methylation landscapes across human cell types	5
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	5
RNA therapeutics	5
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	5
Uridine analogs prevent stress granule formation, not by blocking PKR recognition, but by inhibiting the synthesis of T7 RNA Polymerase byproducts	5
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	5
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	5
Artifacts and biases of the reverse transcription reaction in RNA sequencing	5
Principles, functions, and biological implications of m6A in plants	5
CNOT10 is involved in the TTP-mediated AU-rich element-containing mRNA metabolism, independent of mRNA decay regulation	4
TheEscherichia coli ribBriboswitch senses flavin mononucleotide within a defined transcriptional window	4
5′ UTR cis -regulatory logic governs ribosome engagement on canonical and noncoding RNAs	4
Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics	4
T helper cells exhibit a dynamic and reversible 3′-UTR landscape	4
An MST-based assay reveals new binding preferences of IFIT1 for canonically and noncanonically capped RNAs	4
Protein binding in an mRNA 5′-UTR sterically hinders translation	4
tRNATyrhas an unusually short half-life inTrypanosoma brucei	4
Optimal stability of a highly conserved RNA G4 in PDCoV nsp8 supports viral proliferation	4
Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei	4
ADARs mediate distinct RNA editing activity and gene regulation in the Caenorhabditis elegans germline	4
Z-RNA biology: a central role in the innate immune response?	4
eIF4F-mediated dysregulation of mRNA translation in cancer	4
SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data	4
RNase L produces tRNA-derived RNAs that contribute to translation inhibition	4
Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods	4
lncRNA BC200 is processed into a stable Alu monomer	4
NMDtxDB: data-driven identification and annotation of human NMD target transcripts	4
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	4
Quantitative comparison of methodologies for translation site imaging in living cells	4
A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker)	4