RNA

Article	Citations
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	101
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	101
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	83
Oppositional poly(A) tail length regulation by FMRP and CPEB1	79
Molecular basis for GIGYF–TNRC6 complex assembly	76
Motifs in SARS-CoV-2 evolution	72
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	67
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	58
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	55
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	52
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	51
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	51
Nuclear RNA-binding proteins meet cytoplasmic viruses	46
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	46
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	45
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	45
The total mRNA concentration buffering system in yeast is global rather than gene-specific	43
Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor	41
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	41
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	40
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	38
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	35
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	33
Far from home: the role of glial mRNA localization in synaptic plasticity	30
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	29

Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion	29
The m6A-binding protein YTHDF3 modulates the cardiac response to stress	28
A novel reporter for helicase activity in translation uncovers DDX3X interactions	28
Exploring the targeting spectrum of rocaglates among eIF4A homologs	25
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	25
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	25
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	24
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	24
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	24
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	24
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	24
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	23
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals	23
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	23
Diversity and modularity of tyrosine-accepting tRNA-like structures	23
Adenosine deaminases that act on RNA, then and now	22
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	22
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	22
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	22
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	21
Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing.	20
clipplotr—a comparative visualization and analysis tool for CLIP data	20
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	20
Absolute Quantification of Mammalian MicroRNAs for Therapeutic RNA Cleavage and Detargeting	20
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	20
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	20
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	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
DDX3X and DDX3Y are redundant in protein synthesis	20
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	20
Translation elongation inhibitors stabilize select short-lived transcripts	19
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	19
The limits of human microRNA annotation have been met	19
Localization of RNAs to the Mitochondria – Mechanisms and Functions	19
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA	19
An incredible life in science: Joseph G. Gall (1928–2024)	19
Boosting the toolbox for live imaging of translation	18
The pseudotorsional space of RNA	18
SMDesigner: a program to design sequence mutations to assess RNA structure	18
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	17
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	17
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	17
RNA modifications: an overview of select web-based tools	17
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	17
Corrigendum: No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV, and MLV viral RNA	17
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	16
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53 mediated tumor suppression	16
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	16
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	16

Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	16
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	16
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	16
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	15
Implications for OLE RNA as a natural integral membrane RNA	15
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	15
OpenASO: RNA Rescue — designing splice-modulating antisense oligonucleotides through community science	15
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	15
Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc7	15
Walter Keller (1938–2023): a tribute from his mentees	14
The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode	14
The daunting task of modifying ribosomal RNA	14
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	14
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	14
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	14
DNMT1 inhibition by pUG-fold quadruplex RNA	14
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	14
ac4C: a fragile modification with stabilizing functions in RNA metabolism	14
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	14
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	13
Conformational dynamics of the hepatitis C virus 3′X RNA	13
RNA G-quadruplex structure targeting and imaging: recent advances and future directions	13
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	13
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence	13
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	13
Understanding the redundant functions of the m6A-binding YTHDF proteins	13
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	13
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	13
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	12
Chemical manipulation of m1A mediates its detection in human tRNA	12
Computational design and experimental verification of pseudoknotted ribozymes	12
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	12
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	12
Molecular basis of human polyA polymerase recruitment by mPSF	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
Alternative splicing regulation of membrane trafficking genes during myogenesis	11
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	11
KRGG1 function in RNA editing inTrypanosoma brucei	11
The unfolding landscape of RNA and disease	11
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	11
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	11
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	11
RNA gain-of-function mechanisms in short tandem repeat diseases	10
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	10
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	10
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	10
Targeting splicing factors for cancer therapy	10
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	10
SnoRNA guide activities: real and ambiguous	10
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	10
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	10
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	10
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs	10
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	10
RNA sequence and structure control assembly and function of RNA condensates	10
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	10
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of theBDF2mRNA	9
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development	9
The life and times of a tRNA	9
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	9
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations	9
T1TAdb: the database of type I toxin–antitoxin systems	9
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae	9
Theje ne sais quoiof 5-methylcytosine in messenger RNA	9
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	9
Antisense modulation of IL7R splicing to control sIL7R expression in human CD4+T cells	9
RNA aptamers as tools for the purification and analysis of in vivo assembled Ribonucleoproteins	9
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	9
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome	9
Tribute to Yoshiro Shimura (1932–2023)	9
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging	9
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures	8
Is there a localized role for translational quality control?	8
Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E	8
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging	8
Quantification of tRNA m1A modification by templated-ligation qPCR	8
On the origin of life: an RNA-focused synthesis and narrative	8

Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease	8
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	8
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells	8
Crystal structures of free-state tRNALeu reveal conformational flexibility of Type-II tRNAs	8
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing	8
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data	8
The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements	8
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line	8
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast	8
Design considerations for analyzing protein translation regulation by condensates	8
Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members	8
Alu RNA pseudoknot alterations influence SRP9/SRP14 association	8
Robo-Therm, a pipeline to RNA Thermometer discovery and validation	8
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq	8
Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development	8
Examining SRP pathway function in mRNA localization to the endoplasmic reticulum	8
Human T-cell leukemia virus type 1 uses a specific tRNAProisodecoder to prime reverse transcription	8
Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes	7
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	7
Dissecting the stress granule RNA world: dynamics, strategies, and data	7
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	7
RNA therapeutics	7
A crescendo of competent coding (c3) contains the Standard Genetic Code	7
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding	7
Recollections: Yasuhiro Furuichi (1940–2022)	7
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	7
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	7
2′-O-methylation (Nm) in RNA: progress, challenges, and future directions	7
Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation	7
RNA in biological condensates	7
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	7
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	6
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	6
The universally conserved nucleotides of the small subunit ribosomal RNAs	6
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	6
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	6
In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans	6
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection	6
Artifacts and biases of the reverse transcription reaction in RNA sequencing	6
Fungi of the order Mucorales express a “sealing-only” tRNA ligase	6
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	6
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance	6
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	6
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization	6
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	6
Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling	6
A general and biomedical perspective of viral quasispecies	6
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	6
Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts	6
Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression	5
Principles, functions, and biological implications of m6A in plants	5
The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes	5
The Pet127 protein is a mitochondrial 5′-to-3′ exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts	5
NMDtxDB: data-driven identification and annotation of human NMD target transcripts	5
How do protein domains of low sequence complexity work?	5
Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei	5
Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides	5
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43	5
Anionic G•U pairs in bacterial ribosomal rRNAs	5
Challenges to mapping and defining m6A function in viral RNA	5
FISH-quant v2: a scalable and modular tool for smFISH image analysis	5
Biochemical characterization of mRNA capping enzyme from Faustovirus	5
TheEscherichia coli ribBriboswitch senses flavin mononucleotide within a defined transcriptional window	5
Expansion and functional analysis of the SR-related protein family across the domains of life	5
Development, validation, and application of the ribosome separation and reconstitution system for protein translation in vitro	5
Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing	5
lncRNA BC200 is processed into a stable Alu monomer	5
Principles, mechanisms, and biological implications of translation termination–reinitiation	5
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex	5
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA	5
Corrigendum: Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium	5
DRBD18 acts as a transcript-specific RNA editing auxiliary factor inTrypanosoma brucei	5
A general RNA-templated RNA extension activity of E. coli RNA polymerase	5
RNase L produces tRNA-derived RNAs that contribute to translation inhibition	5
Z-RNA biology: a central role in the innate immune response?	5
Sod1-deficient cells are impaired in formation of the modified nucleosides mcm5s2U and yW in tRNA	5
tRNATyrhas an unusually short half-life inTrypanosoma brucei	5
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	5
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	5
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	4
RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits inStaphylococcus aureus	4
Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions	4
RNA-binding proteins in disease etiology: fragile X syndrome and spinal muscular atrophy	4
Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism	4
Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation	4
Identification of leader–trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea	4
lncRNAMalat1and miR-26 cooperate in the regulation of neuronal progenitor cell proliferation and differentiation	4
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing	4
Beyond RNA-binding domains: determinants of protein–RNA binding	4
Translational control byTrypanosoma bruceiDRBD18 contributes to the maintenance of the procyclic state	4
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection	4
Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets	4
The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells	4
Which came first: the chicken, the egg, or guanine?	4
tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT1	4