RNA

Article	Citations
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	95
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	95
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	81
Molecular basis for GIGYF–TNRC6 complex assembly	70
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	69
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	66
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	62
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	53
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	51
Motifs in SARS-CoV-2 evolution	48
Oppositional poly(A) tail length regulation by FMRP and CPEB1	48
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	47
Nuclear RNA-binding proteins meet cytoplasmic viruses	43
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	43
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	43
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	41
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	41
The m6A binding protein YTHDF3 modulates the cardiac response to stress	40
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	39
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	38
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	38
Far from home: the role of glial mRNA localization in synaptic plasticity	37
A novel reporter for helicase activity in translation uncovers DDX3X interactions	35
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering	33
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	32

The total mRNA concentration buffering system in yeast is global rather than gene-specific	30
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	28
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	28
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	27
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	27
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	26
Exploring the targeting spectrum of rocaglates among eIF4A homologs	25
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	25
Adenosine deaminases that act on RNA, then and now	24
Diversity and modularity of tyrosine-accepting tRNA-like structures	23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	23
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function	23
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	23
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	23
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	22
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	22
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	22
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes	21
Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNAIle(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA	21
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP	21
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	21
clipplotr—a comparative visualization and analysis tool for CLIP data	20
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining	20
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities	20
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)	19
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	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
The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication	19
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions	19
Localization of RNAs to the Mitochondria – Mechanisms and Functions	19
DDX3X and DDX3Y are redundant in protein synthesis	19
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	19
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs	19
Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc7	18
Translation elongation inhibitors stabilize select short-lived transcripts	18
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	18
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity	18
The limits of human microRNA annotation have been met	18
The pseudotorsional space of RNA	18
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells	18
Boosting the toolbox for live imaging of translation	18
SMDesigner: a program to design sequence mutations to assess RNA structure	18
Corrigendum: No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV, and MLV viral RNA	17
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	17
RNA modifications: an overview of select web-based tools	17
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers	17
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription	17
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	17
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	16

Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2	16
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila	16
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	16
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	16
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation	16
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	15
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	15
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	15
The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode	14
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	14
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	14
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	14
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence	14
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	14
Walter Keller (1938–2023): a tribute from his mentees	14
Understanding the redundant functions of the m6A-binding YTHDF proteins	14
The daunting task of modifying ribosomal RNA	14
Conformational dynamics of the hepatitis C virus 3′X RNA	13
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	13
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	13
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	13
Chemical manipulation of m1A mediates its detection in human tRNA	13
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	13
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	12
ac4C: a fragile modification with stabilizing functions in RNA metabolism	12
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	12
The unfolding landscape of RNA and disease	12
DNMT1 inhibition by pUG-fold quadruplex RNA	12
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	12
Molecular basis of human polyA polymerase recruitment by mPSF	12
Computational design and experimental verification of pseudoknotted ribozymes	12
RNA gain-of-function mechanisms in short tandem repeat diseases	12
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	12
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	11
KRGG1 function in RNA editing inTrypanosoma brucei	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	11
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs	11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
IsoSplitter: identification and characterization of alternative splicing sites without a reference genome	11
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	11
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	11
Targeting splicing factors for cancer therapy	11
Alternative splicing regulation of membrane trafficking genes during myogenesis	11
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target	10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	10
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea	10
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	10
SnoRNA guide activities: real and ambiguous	10
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	10
Theje ne sais quoiof 5-methylcytosine in messenger RNA	10
APOBEC1 mediated C-to-U RNA editing: target sequence and trans-acting factor contribution to 177 RNA editing events in 119 murine transcripts in vivo	10
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	10
RNA sequence and structure control assembly and function of RNA condensates	10
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	10
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development	9
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae	9
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	9
Human T-cell leukemia virus type 1 uses a specific tRNAProisodecoder to prime reverse transcription	9
The life and times of a tRNA	9
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome	9
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae	9
Rational design yields RNA-binding zinc finger domains with altered sequence specificity	9
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging	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
T1TAdb: the database of type I toxin–antitoxin systems	9
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders	9
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of theBDF2mRNA	9
Tribute to Yoshiro Shimura (1932–2023)	9
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	9
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations	9
Design considerations for analyzing protein translation regulation by condensates	8
Is there a localized role for translational quality control?	8
Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members	8
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures	8
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq	8
The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements	8
Quantification of tRNA m1A modification by templated-ligation qPCR	8
Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation	8
Examining SRP pathway function in mRNA localization to the endoplasmic reticulum	8

Antisense modulation of IL7R splicing to control sIL7R expression in human CD4+T cells	8
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast	8
Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E	8
Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes	8
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding	8
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease	8
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line	8
The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes	8
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells	8
Robo-Therm, a pipeline to RNA Thermometer discovery and validation	8
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing	8
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging	8
RNA therapeutics	7
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	7
On the origin of life: an RNA-focused synthesis and narrative	7
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	7
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation	7
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	7
Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation	7
RNA in biological condensates	7
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA	7
2′-O-methylation (Nm) in RNA: progress, challenges, and future directions	7
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	7
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	7
Recollections: Yasuhiro Furuichi (1940–2022)	7
Dissecting the stress granule RNA world: dynamics, strategies and data	7
A crescendo of competent coding (c3) contains the Standard Genetic Code	7
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	7
Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development	7
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	7
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	7
A general and biomedical perspective of viral quasispecies	6
Fungi of the order Mucorales express a “sealing-only” tRNA ligase	6
Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts	6
In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans	6
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	6
Artifacts and biases of the reverse transcription reaction in RNA sequencing	6
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance	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
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization	6
Principles, functions, and biological implications of m6A in plants	6
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	6
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	6
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	6
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection	6
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
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	5
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	5
Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing	5
Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei	5
Development, validation, and application of the ribosome separation and reconstitution system for protein translation in vitro	5
A general RNA-templated RNA extension activity of E. coli RNA polymerase	5
Principles, mechanisms, and biological implications of translation termination–reinitiation	5
Challenges to mapping and defining m6A function in viral RNA	5
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43	5
Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression	5
Expansion and functional analysis of the SR-related protein family across the domains of life	5
tRNATyrhas an unusually short half-life inTrypanosoma brucei	5
Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides	5
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20	5
Biochemical characterization of mRNA capping enzyme from Faustovirus	5
CRED9: a differentially expressed elncRNA regulates expression of transcription factor CEBPA	5
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex	5
Anionic G•U pairs in bacterial ribosomal rRNAs	5
TheEscherichia coli ribBriboswitch senses flavin mononucleotide within a defined transcriptional window	5
Sod1-deficient cells are impaired in formation of the modified nucleosides mcm5s2U and yW in tRNA	5
lncRNA BC200 is processed into a stable Alu monomer	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
DRBD18 acts as a transcript-specific RNA editing auxiliary factor inTrypanosoma brucei	5
The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes	5
How do protein domains of low sequence complexity work?	4
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	4
Replication of alphaviruses requires a pseudoknot that involves the poly(A) tail	4
RNA-binding proteins in disease etiology: fragile X syndrome and spinal muscular atrophy	4
RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits inStaphylococcus aureus	4
Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism	4
Which came first: the chicken, the egg, or guanine?	4
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection	4
NMDtxDB: data-driven identification and annotation of human NMD target transcripts	4
Z-RNA biology: a central role in the innate immune response?	4
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	4
Pathological phase transitions in ALS-FTD impair dynamic RNA–protein granules	4
tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT1	4
Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei	4
Beyond RNA-binding domains: determinants of protein–RNA binding	4
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing	4
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique	4
RNase L Produces tRNA-derived RNAs that Contribute to Translation Inhibition	4
Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics	4
Identification of leader–trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea	4
Translational control byTrypanosoma bruceiDRBD18 contributes to the maintenance of the procyclic state	4
Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery	4
CMTr mediated 2′-O-ribose methylation status of cap-adjacent nucleotides across animals	4