RNA

Article	Citations
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	117
Motifs in SARS-CoV-2 evolution	111
Oppositional poly(A) tail length regulation by FMRP and CPEB1	99
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	94
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	78
Simultaneous detection of the AAV genomes and their transcripts in situ at the single-cell level	73
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	58
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	56
Molecular basis for GIGYF–TNRC6 complex assembly	54
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	51
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	50
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	47
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	37
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	33
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	33
Exploring the targeting spectrum of rocaglates among eIF4A homologs	31
Nuclear RNA-binding proteins meet cytoplasmic viruses	30
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	30
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	28
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	28
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	27
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor	27
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	27
Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2	27
The m6A-binding protein YTHDF3 modulates the cardiac response to stress	26

Far from home: the role of glial mRNA localization in synaptic plasticity	26
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	26
A novel reporter for helicase activity in translation uncovers DDX3X interactions	25
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	25
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	24
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	24
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	24
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	23
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	23
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	23
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	22
Diversity and modularity of tyrosine-accepting tRNA-like structures	22
Adenosine deaminases that act on RNA, then and now	22
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	22
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	21
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	21
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	21
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	21
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	20
clipplotr—a comparative visualization and analysis tool for CLIP data	20
Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNAIle(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA	20
Novel ADAR2 variants in children with seizures, intellectual disability, and motor delay have reduced RNA editing	20
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	20
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	19
An incredible life in science: Joseph G. Gall (1928–2024)	19
Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting	19
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	19
PACT suppresses PKR activation through dsRNA binding and dimerization, and is a therapeutic target for triple-negative breast cancer	19
SMDesigner: a program to design sequence mutations to assess RNA structure	18
The pseudotorsional space of RNA	18
Desthiobiotin (DTB)-modified and TAMRA-modified 2''OMeNAD+ are RNA 2'-phosphotransferase (Tpt1) poisons that enable affinity-tagging and fluorescence-tagging of internal RNA 2'-phosphate gr	18
The limits of human microRNA annotation have been met	18
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	18
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	17
Translation elongation inhibitors stabilize select short-lived transcripts	17
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	17
The codon context provides cis-acting immune evasion for the human papilloma virus (HPV) E6	17
Boosting the toolbox for live imaging of translation	17
Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery	17
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	16
Localization of RNAs to the Mitochondria – Mechanisms and Functions	16
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	15
RNA modifications: an overview of select web-based tools	15
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	15
Corrigendum: No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV, and MLV viral RNA	15
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	15
Solution Structure Determination and Biophysical Studies of 7SK RNP and 7SL SRP RNAs	14
Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc7	14
OpenASO: RNA Rescue—designing splice-modulating antisense oligonucleotides through community science	14

Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	14
Three critical regions of the erythromycin resistance methyltransferase, ErmE, are required for function supporting a model for the interaction of Erm family enzymes with substrate rRNA	14
Implications for OLE RNA as a natural integral membrane RNA	14
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	14
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	13
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53-mediated tumor suppression	13
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	13
Walter Keller (1938–2023): a tribute from his mentees	13
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	13
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	13
C. elegans FBF-1 and FBF-2 C-terminal intrinsically-disordered regions differentially regulate RNA-binding affinity	13
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	13
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	13
Computational design and experimental verification of pseudoknotted ribozymes	12
Conformational dynamics of the hepatitis C virus 3′X RNA	12
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	12
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	12
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	12
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	12
The daunting task of modifying ribosomal RNA	12
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	12
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	12
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	12
ac4C: a fragile modification with stabilizing functions in RNA metabolism	11
Understanding the redundant functions of the m6A-binding YTHDF proteins	11
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	11
RNA G-quadruplex structure targeting and imaging: recent advances and future directions	11
DNMT1 inhibition by pUG-fold quadruplex RNA	11
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	11
ZYS-1 is not an ADAR1 inhibitor	11
Chemical manipulation of m1A mediates its detection in human tRNA	11
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	11
The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode	11
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	11
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	11
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence	11
KRGG1 function in RNA editing inTrypanosoma brucei	11
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	10
Alternative splicing regulation of membrane trafficking genes during myogenesis	10
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	10
Targeting splicing factors for cancer therapy	10
RNA gain-of-function mechanisms in short tandem repeat diseases	10
Study of the RNA splicing kinetics via in vivo 5-EU labeling	10
The role of Nonsense-Mediated mRNA Decay in restricting long noncoding RNAs expression has been conserved in RNAi-capable budding yeast	10
The unfolding landscape of RNA and disease	10
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	10
Molecular basis of human polyA polymerase recruitment by mPSF	10
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	10
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	10
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	10
Promiscuous RNA editing in lncRNA roX1 is generally non-adaptive	10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	9
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	9
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	9
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	9
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome	9
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	9
Splice site diversity and abundance of non-canonical introns in diplonemids (Diplonemea, Euglenozoa)	9
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	9
RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins	9
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	9
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	9
Theje ne sais quoiof 5-methylcytosine in messenger RNA	9
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae	9
Tribute to Yoshiro Shimura (1932–2023)	8
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3′-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides	8
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development	8
Human T-cell leukemia virus type 1 uses a specific tRNAProisodecoder to prime reverse transcription	8
Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members	8
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast	8
The life and times of a tRNA	8
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	8
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line	8
Interdomain assembly between the fungal tRNA ligase adenylyltransferase and kinase domain	8
Is there a localized role for translational quality control?	8
Crystal structures of free-state tRNALeu reveal conformational flexibility of type-II tRNAs	8
Antisense modulation of IL7R splicing to control sIL7R expression in human CD4+T cells	8
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	8
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations	8
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	8

Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	8
Context-dependent phosphorylation of CSDE1 drives interactions with ribosomes	8
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures	8
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging	7
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing	7
2′-O-methylation (Nm) in RNA: progress, challenges, and future directions	7
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data	7
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding	7
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq	7
Quantification of tRNA m1A modification by templated-ligation qPCR	7
Alu RNA pseudoknot alterations influence SRP9/SRP14 association	7
On the origin of life: an RNA-focused synthesis and narrative	7
Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development	7
Proteins that recognize unique features of U7 snRNA and may substitute for Gemin5 in the assembly of U7-specific Sm ring	7
Robo-Therm, a pipeline to RNA Thermometer discovery and validation	7
40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion	7
Examining SRP pathway function in mRNA localization to the endoplasmic reticulum	7
The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements	7
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells	7
Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes	7
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging	7
Recollections: Yasuhiro Furuichi (1940–2022)	7
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	6
Dissecting the stress granule RNA world: dynamics, strategies, and data	6
ykkC-I Riboswitch Aptamer Domain Requires an Interplay Between Metal Triad and Cationic Ligand: Insights into Metal Ion-Induced Allostery from Molecular Dynamics Simulations	6
Conserved protein Seb1 that interacts with RNA polymerase II and RNA is an anti-pausing transcription elongation factor	6
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	6
RNA in biological condensates	6
A crescendo of competent coding (c3) contains the Standard Genetic Code	6
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	6
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	6
Integrated NMR and MD structure and dynamics of the stem loop II motif (s2m) from the Omicron variant of SARS-CoV-2	6
Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation	6
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	6
RNA therapeutics	6
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	6
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	6
New mechanistic insights into Prespliceosome formation-Roles of DEAD-box proteins Prp5 and Sub2	6
Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts	6
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	6
Principles, mechanisms, and biological implications of translation termination–reinitiation	5
Biochemical characterization of mRNA capping enzyme from Faustovirus	5
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex	5
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43	5
Corrigendum: Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium	5
FISH-quant v2: a scalable and modular tool for smFISH image analysis	5
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	5
Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling	5
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection	5
A general and biomedical perspective of viral quasispecies	5
Vault RNA1–1 riboregulates the autophagic function of p62 by binding to lysine 7 and arginine 21, both of which are critical for p62 oligomerization	5
The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes	5
Challenges to mapping and defining m6A function in viral RNA	5
Polyadenylation landscape of in vivo long-term potentiation in the rat brain	5
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	5
DRBD18 acts as a transcript-specific RNA editing auxiliary factor inTrypanosoma brucei	5
In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans	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
The universally conserved nucleotides of the small subunit ribosomal RNAs	5
Artifacts and biases of the reverse transcription reaction in RNA sequencing	5
Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression	5
Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei	5
Anionic G•U pairs in bacterial ribosomal rRNAs	5
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	5
A general RNA-templated RNA extension activity of E. coli RNA polymerase	5
Fungi of the order Mucorales express a “sealing-only” tRNA ligase	5
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA	5
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	5
Principles, functions, and biological implications of m6A in plants	5
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	5
Which came first: the chicken, the egg, or guanine?	4
Translational control byTrypanosoma bruceiDRBD18 contributes to the maintenance of the procyclic state	4
Beyond RNA-binding domains: determinants of protein–RNA binding	4
lncRNAMalat1and miR-26 cooperate in the regulation of neuronal progenitor cell proliferation and differentiation	4
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	4
tRNATyrhas an unusually short half-life inTrypanosoma brucei	4
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20	4
Protein binding in an mRNA 5′-UTR sterically hinders translation	4
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection	4
Identification of leader–trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea	4
RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits inStaphylococcus aureus	4
T helper cells exhibit a dynamic and reversible 3′-UTR landscape	4
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	4
Sod1-deficient cells are impaired in formation of the modified nucleosides mcm5s2U and yW in tRNA	4
High-throughput imaging of mRNA at the single-cell level in human primary immune cells	4
Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics	4
The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells	4
CMTr mediated 2′-O-ribose methylation status of cap-adjacent nucleotides across animals	4
RNA-binding proteins in disease etiology: fragile X syndrome and spinal muscular atrophy	4
eIF4F-mediated dysregulation of mRNA translation in cancer	4
Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets	4
Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2′-PO4splice junction versus a 5′-PO4mononucleotide	4
An MST-based assay reveals new binding preferences of IFIT1 for canonically and noncanonically capped RNAs	4
SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data	4