RNA

Article	Citations
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly	74
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity	72
Turn-on RNA Mango Beacons fortrans-acting fluorogenic nucleic acid detection	68
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors	52
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability	51
Cellular translational enhancer elements that recruit eukaryotic initiation factor 3	49
The daunting task of modifying ribosomal RNA	48
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p	46
RNA in biological condensates	45
Walter Keller (1938–2023): a tribute from his mentees	43
In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome	40
Direct dsRNA preparation by promoter-free RCT and RNase H cleavage using one circular dsDNA template with a mismatched bubble	38
Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNAVal	37
Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components	37
Recollections: Yasuhiro Furuichi (1940–2022)	37
HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs	36
Suppression of theEscherichia coli rnpA49conditionally lethal phenotype by different compensatory mutations	30
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	30
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis	29
A crescendo of competent coding (c3) contains the Standard Genetic Code	29
Motifs in SARS-CoV-2 evolution	29
Genome-wide kinetic profiling of pre-mRNA 3′ end cleavage	28
Tho2 is critical for the recruitment of Rrp6 to chromatin in response to perturbed mRNP biogenesis	27
Impact on splicing inSaccharomyces cerevisiaeof random 50-base sequences inserted into an intron	26
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning	25

Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro	24
Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia	24
Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs	23
The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode	23
Erratum: Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	23
Molecular basis for GIGYF–TNRC6 complex assembly	23
Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH	23
Computational design and experimental verification of pseudoknotted ribozymes	23
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	21
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?	20
Oppositional poly(A) tail length regulation by FMRP and CPEB1	20
Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3′ splice site usage	19
A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation	19
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2	18
Function and mechanism of action of the small regulatory RNA ArcZ inEnterobacterales	18
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution	18
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis	18
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF	18
The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation	18
Hammerhead ribozyme-based U-insertion and deletion RNA editing assays for multiplexing in HTS applications	18
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex	17
Balanced cell division is secured by two different regulatory sites in OxyS RNA	17
Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions	17
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses	17
RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions	16
Widespread destabilization ofCaenorhabditis elegansmicroRNAs by the E3 ubiquitin ligase EBAX-1	16
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis	16
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data	15
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	15
N6-methyladenosine reader YTHDF2 in cell state transition and antitumor immunity	15
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	15
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1	15
RNA therapeutics	15
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions	15
Processing and decay of 6S-1 and 6S-2 RNAs inBacillus subtilis	15
Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inBacillus subtilis	15
VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets	15
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	15
Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase	14
Conformational dynamics of the hepatitis C virus 3′X RNA	14
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	14
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals	14
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends	14
Chemical manipulation of m1A mediates its detection in human tRNA	14
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	14
Widespread genetic heterogeneity of human ribosomal RNA genes	14
Applications and future of aptamers that achieve rapid-onset anticoagulation	14
ac4C: a fragile modification with stabilizing functions in RNA metabolism	14
Alternative splicing factors and cardiac disease: more than just mis-splicing?	13
Global analysis by LC-MS/MS of N6-methyladenosine and inosine in mRNA reveal complex incidence	13

The landscape of translational stall sites in bacteria revealed by monosome and disome profiling	13
Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning	13
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	13
RNA sensing at the crossroads of autoimmunity and autoinflammation	13
RNALigands: a database and web server for RNA–ligand interactions	13
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	13
bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling	12
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein	12
Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis	12
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations	12
DNMT1 inhibition by pUG-fold quadruplex RNA	12
Understanding the redundant functions of the m6A-binding YTHDF proteins	12
The ribosome epitranscriptome: inert—or a platform for functional plasticity?	12
The role of stress-activated RNA–protein granules in surviving adversity	12
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging	11
Nanopore sequencing of internal 2′-PO4modifications installed by RNA repair	11
Kinetic dissection of pre-crRNA binding and processing by CRISPR–Cas12a	11
New reporters for monitoring cellular NMD	11
Meeting report ASOBIOTICS 2024: an interdisciplinary symposium on antisense-based programmable RNA antibiotics	11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company	11
Characterization of tRNA splicing enzymes RNA ligase and tRNA 2′-phosphotransferase from the pathogenic fungi Mucorales	11
Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation	11
Study of the RNA splicing kinetics via in vivo 5-EU labeling	11
AptaDB: a comprehensive database integrating aptamer–target interactions	10
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast	10
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans	10
Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors	10
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria	10
Exploring the targeting spectrum of rocaglates among eIF4A homologs	10
Molecular basis of human polyA polymerase recruitment by mPSF	10
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	10
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	10
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures	10
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	10
KRGG1 function in RNA editing inTrypanosoma brucei	10
Evolutionary divergence of Firre localization and expression	9
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells	9
IsoSplitter: identification and characterization of alternative splicing sites without a reference genome	9
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations	9
Mouse nuclear RNAi-defective 2 promotes splicing of weak 5′ splice sites	9
miR-7 is recruited to the high molecular weight RNA-induced silencing complex in CD8+T cells upon activation and suppresses IL-2 signaling	9
Ancestry of RNA/RNA interaction regions within segmented ribosomes	9
Fission yeast poly(A) polymerase active site mutation Y86D alleviates therad24Δasp1-H397Asynthetic growth defect and up-regulates mRNAs targeted by MTREC and Mmi1	9
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells	9
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	9
Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA	9
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance	9
Analysis of GTP addition in the reverse (3′–5′) direction by human tRNAHis guanylyltransferase	9
A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex	9
Phase-separated ribosome-nascent chain complexes in genotoxic stress response	9
NUCLEAR RNA-BINDING PROTEINS MEET CYTOPLASMIC VIRUSES	8
Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms	8
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae	8
Biochemical and genetic dissection of the RNA-binding surface of the FinO domain ofEscherichia coliProQ	8
Alternative splicing regulation of membrane trafficking genes during myogenesis	8
In vivo PIWI slicing in mouse testes deviates from rules established in vitro	8
A novel reporter for helicase activity in translation uncovers DDX3X interactions	8
Extracellular N6-isopentenyladenosine (i6A) addition induces cotranscriptional i6A incorporation into ribosomal RNAs	8
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	8
Methylation guide RNAs without box C/D motifs	8
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA	8
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand	8
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	8
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules	8
circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner	7
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription	7
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection	7
Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents	7
A model for DHX15 mediated disassembly of A-complex spliceosomes	7
The small noncoding RNAVaultrc5is dispensable to mouse development	7
In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans	7
A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS	7
Structure and thermodynamics of a UGG motif interacting with Ba2+and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)–G(syn) pair	7
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes	7
Adaptive sampling for nanopore direct RNA-sequencing	7
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization	7
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	7
RNA:RNA interaction in ternary complexes resolved by chemical probing	7
E. coli 6S RNA complexed to RNA polymerase maintains product RNA synthesis at low cellular ATP levels by initiation with non-canonical initiator nucleotides	7
TheBacillus subtilis ywbDgene encodes RlmQ, the 23S rRNA methyltransferase forming m7G2574 in the A-site of the peptidyl transferase center	7

The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice	7
Far from home: the role of glial mRNA localization in synaptic plasticity	7
Human RNase P: overview of a ribonuclease of interrelated molecular networks and gene-targeting systems	7
Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium	7
Validation and classification of RNA binding proteins identified by mRNA interactome capture	7
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	7
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	7
Development of bioconjugate-based delivery systems for nucleic acids	6
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	6
Ensemble switching unveils a kinetic rheostat mechanism of the eukaryotic thiamine pyrophosphate riboswitch	6
RNA Gain-of-Function Mechanisms in Short Tandem Repeat Diseases	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
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function	6
Site-directed A → I RNA editing as a therapeutic tool: moving beyond genetic mutations	6
The universally conserved nucleotides of the small subunit ribosomal RNAs	6
Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease	6
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity	6
The total mRNA concentration buffering system in yeast is global rather than gene-specific	6
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	6
Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	6
A general and biomedical perspective of viral quasispecies	6
FISH-quant v2: a scalable and modular tool for smFISH image analysis	6
Principles, functions, and biological implications of m6A in plants	5
Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types	5
Targeting splicing factors for cancer therapy	5
U2AF2 binds IL7R exon 6 ectopically and represses its inclusion	5
Corrigendum: Specific roles for the Ccr4-Not complex subunits in expression of the genome	5
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation	5
Characterization of Cwc2, U6 snRNA, and Prp8 interactions destabilized by Prp16 ATPase at the transition between the first and second steps of splicing	5
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	5
Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing	5
SRSF10: an atypical splicing regulator with critical roles in stress response, organ development, and viral replication	5
Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium	5
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast	5
Revisiting tRNA chaperones: new players in an ancient game	5
Tribute to Sidney AltmanSIDNEY ALTMAN: AN EXEMPLARY SCIENTIST, TEACHER, AND FRIEND (1939–2022)SIDNEY ALTMAN'S GREATEST ACHIEVEMENTA SHORT HISTORY OF THE DISCOVERY OF THE ESSENTIAL RNA COMPONENT OF RNa	5
A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations	5
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs	4
Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination	4
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	4
The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes	4
Diversity and modularity of tyrosine-accepting tRNA-like structures	4
Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay	4
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	4
Single-cell transcriptome sequencing on the Nanopore platform with ScNapBar	4
Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome	4
ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5′ splice site motifs within nuclear speckles	4
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	4
Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry	4
Drop-off-reinitiation at the amino termini of nascent peptides and its regulation by IF3, EF-G, and RRF	4
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43	4
No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA	4
Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability	4
A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism inSaccharomyces cerevisiae	4
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression	4
RNA sequence and structure control assembly and function of RNA condensates	4
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA	4
Biochemical characterization of mRNA capping enzyme from Faustovirus	4
An improved in vivo tethering assay with single molecule FISH reveals that a nematode Nanos enhances reporter expression and mRNA stability	4
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	4
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	4
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements	4
tRNAValallows four-way decoding with unmodified uridine at the wobble position inLactobacillus casei	4
CRED9: a differentially expressed elncRNA regulates expression of transcription factor CEBPA	4
High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high confidence identification of RNA binding proteins	4
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions	4
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	4
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex	4
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	4
Corrigendum: Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium	4
rRFtargetDB: a database of Ago1-mediated targets of ribosomal RNA fragments	3
Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs	3
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	3
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	3
Principles, mechanisms, and biological implications of translation termination–reinitiation	3
The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation	3
DRBD18 acts as a transcript-specific RNA editing auxiliary factor inTrypanosoma brucei	3
Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements	3
Structural and functional effects of inosine modification in mRNA	3
Structure and ion-dependent folding of k-junctions	3
Using quantitative reconstitution to investigate multicomponent condensates	3
Sensing of transposable elements by the antiviral innate immune system	3
Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA counterpart in terminal hematopoiesis	3
Quantification of elongation stalls and impact on gene expression in yeast	3
Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides	3
Structure of the dengue virus RNA promoter	3
Challenges to mapping and defining m6A function in viral RNA	3
Anionic G•U pairs in bacterial ribosomal rRNAs	3
A versatile tRNA modification-sensitive northern blot method with enhanced performance	3
Direct and indirect control of Rho-dependent transcription termination by theEscherichia coli lysCriboswitch	3
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique	3
Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation	3
Cytoplasmic Regulation of the Poly(A) Tail Length as a Potential Therapeutic Target	3
Adenosine deaminases that act on RNA, then and now	3