RNA

Article	Citations
The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation	105
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	72
The emerging structural complexity of G-quadruplex RNAs	72
RNA in formation and regulation of transcriptional condensates	68
FISH-quant v2: a scalable and modular tool for smFISH image analysis	63
RNA partitioning into stress granules is based on the summation of multiple interactions	62
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	52
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	47
The virtual circular genome model for primordial RNA replication	46
The life and times of a tRNA	44
Sensing of transposable elements by the antiviral innate immune system	43
DDX3X and DDX3Y are redundant in protein synthesis	42
Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem?	40
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	40
Are stress granules the RNA analogs of misfolded protein aggregates?	39
Long noncoding RNA and protein abundance in lncRNPs	38
RNA multimerization as an organizing force for liquid–liquid phase separation	37
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein	37
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome	37
How do protein domains of low sequence complexity work?	36
Cyclic oligoadenylate signaling and regulation by ring nucleases during type III CRISPR defense	36
Circulating SNORD57 rather than piR-54265 is a promising biomarker for colorectal cancer: common pitfalls in the study of somatic piRNAs in cancer	32
Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot	30
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?	29
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions	29

Exploring the epitranscriptome by native RNA sequencing	29
Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA	28
Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules	28
Rampant C-to-U deamination accounts for the intrinsically high mutation rate in SARS-CoV-2 spike gene	27
RNA sequence and structure control assembly and function of RNA condensates	27
Review of single-cell RNA-seq data clustering for cell-type identification and characterization	26
A mark of disease: how mRNA modifications shape genetic and acquired pathologies	26
Cold-inducible RNA binding protein promotes breast cancer cell malignancy by regulating Cystatin C levels	26
Argonaute binding within human nuclear RNA and its impact on alternative splicing	25
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET	25
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	24
The limits of human microRNA annotation have been met	24
Ensemble switching unveils a kinetic rheostat mechanism of the eukaryotic thiamine pyrophosphate riboswitch	23
Nuage condensates: accelerators or circuit breakers for sRNA silencing pathways?	23
A model for DHX15 mediated disassembly of A-complex spliceosomes	23
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	23
Revisiting tRNA chaperones: new players in an ancient game	23
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation	23
A second riboswitch class for the enzyme cofactor NAD+	22
mRNA spindle localization and mitotic translational regulation by CPEB1 and CPEB4	21
Using quantitative reconstitution to investigate multicomponent condensates	21
An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7	20
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses	20
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	20
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs	20
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	19
Cotranscriptional splicing efficiencies differ within genes and between cell types	18
RNALigands: a database and web server for RNA–ligand interactions	18
Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon	18
The role of stress-activated RNA–protein granules in surviving adversity	18
Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning	18
Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation	18
PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells	18
Pathological phase transitions in ALS-FTD impair dynamic RNA–protein granules	17
Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation	17
Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics	17
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	17
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique	17
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays	16
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	16
Widespread genetic heterogeneity of human ribosomal RNA genes	16
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	16
Structure of 3′-PO4/5′-OH RNA ligase RtcB in complex with a 5′-OH oligonucleotide	15
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	15
Human spliceosomal snRNA sequence variants generate variant spliceosomes	15
Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA	15
SRSF10: an atypical splicing regulator with critical roles in stress response, organ development, and viral replication	15
RNase H-based analysis of synthetic mRNA 5′ cap incorporation	15
Ribosome profiling reveals novel regulation of C9ORF72 GGGGCC repeat-containing RNA translation	15
Validation and classification of RNA binding proteins identified by mRNA interactome capture	15

A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	15
Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets	15
Acyclic (S)-glycol nucleic acid (S-GNA) modification of siRNAs improves the safety of RNAi therapeutics while maintaining potency	14
A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor	14
Single-cell transcriptome sequencing on the Nanopore platform with ScNapBar	14
Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations	14
T1TAdb: the database of type I toxin–antitoxin systems	14
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions	14
ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5′ splice site motifs within nuclear speckles	14
Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline	14
Transcription and splicing dynamics during early Drosophila development	14
Z-RNA biology: a central role in the innate immune response?	14
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	14
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization	14
Artifacts and biases of the reverse transcription reaction in RNA sequencing	13
Mitochondrial misreading in skeletal muscle accelerates metabolic aging and confers lipid accumulation and increased inflammation	13
Deflating the RNA Mg2+ bubble: stereochemistry to the rescue!	13
The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation	13
The total mRNA concentration buffering system in yeast is global rather than gene-specific	13
The ribosome epitranscriptome: inert—or a platform for functional plasticity?	13
Dynamic association of human Ebp1 with the ribosome	13
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	13
Targeting splicing factors for cancer therapy	13
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals	13
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20	13
The stem cell–specific protein TRIM71 inhibits maturation and activity of the prodifferentiation miRNA let-7 via two independent molecular mechanisms	12
N2 modified dinucleotide cap analogs as a potent tool for mRNA engineering	12
Mutations in domain IV of elongation factor EF-G confer −1 frameshifting	12
Human RNase P: overview of a ribonuclease of interrelated molecular networks and gene-targeting systems	12
PABPN1 prevents the nuclear export of an unspliced RNA with a constitutive transport element and controls human gene expression via intron retention	12
RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands	12
The universally conserved nucleotides of the small subunit ribosomal RNAs	12
bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling	12
Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites	12
Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)	12
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses	12
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	12
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease	11
The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication	11
siRNA potency enhancement via chemical modifications of nucleotide bases at the 5′-end of the siRNA guide strand	11
DNMT1 inhibition by pUG-fold quadruplex RNA	11
Saccharomyces cerevisiae Ecm2 modulates the catalytic steps of pre-mRNA splicing	11
Roadblock-qPCR: a simple and inexpensive strategy for targeted measurements of mRNA stability	11
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	11
The landscape of translational stall sites in bacteria revealed by monosome and disome profiling	11
Future directions for medicinal chemistry in the field of oligonucleotide therapeutics	11
A survey of RNA editing at single-cell resolution links interneurons to schizophrenia and autism	11
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	11
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	11
Structure of the dengue virus RNA promoter	10
Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors	10
Biological solution conditions and flanking sequence modulate LLPS of RNA G-quadruplex structures	10
KDM3A regulates alternative splicing of cell-cycle genes following DNA damage	10
Type III-A CRISPR systems as a versatile gene knockdown technology	10
Principles, mechanisms, and biological implications of translation termination–reinitiation	10
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	10
RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery	10
ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations	10
An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies	10
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	10
Disease-associated mutations in mitochondrial precursor tRNAs affect binding, m1R9 methylation, and tRNA processing by mtRNase P	10
Expansion and functional analysis of the SR-related protein family across the domains of life	10
VfoldMCPX: predicting multistrand RNA complexes	9
On the origin of life: an RNA-focused synthesis and narrative	9
Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis	9
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	9
U2AF2 binds IL7R exon 6 ectopically and represses its inclusion	9
Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA	9
Transcriptional profiling of fission yeast RNA polymerase II CTD mutants	9
The Bacillus subtilis open reading frame ysgA encodes the SPOUT methyltransferase RlmP forming 2′-O-methylguanosine at position 2553 in the A-loop of 23S rRNA	9
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations	9
A versatile tRNA modification-sensitive northern blot method with enhanced performance	9
Site-directed A → I RNA editing as a therapeutic tool: moving beyond genetic mutations	9
Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase	9
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations	9
Transcription-dependent enrichment of the yeast FACT complex influences nucleosome dynamics on the RNA polymerase III-transcribed genes	9
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis	9
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	9
Evolutionary divergence of Firre localization and expression	9
RNA therapeutics	9

Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity	8
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	8
OTTER, a new method for quantifying absolute amounts of tRNAs	8
Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery	8
Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation	8
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2	8
Recoding UAG to selenocysteine inSaccharomyces cerevisiae	8
tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT1	8
Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei	8
Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation	8
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	8
Expansion segments in bacterial and archaeal 5S ribosomal RNAs	8
Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5′ splice sites	8
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	8
The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes	8
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server	7
Extracellular N6-isopentenyladenosine (i6A) addition induces cotranscriptional i6A incorporation into ribosomal RNAs	7
A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its function in hematopoietic differentiation	7
Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E	7
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA	7
Design considerations for analyzing protein translation regulation by condensates	7
The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase binding in 40S ribosome assembly	7
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	7
Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inBacillus subtilis	7
Oppositional poly(A) tail length regulation by FMRP and CPEB1	7
Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis	7
Trans-spliced mRNA products produced from circRNA expression vectors	7
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells	7
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	7
In vivo PIWI slicing in mouse testes deviates from rules established in vitro	7
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand	7
Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5′ end of the siRNA guide strand	7
Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism	7
The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation	7
Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene	7
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	7
RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing	6
Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain	6
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA	6
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development	6
CtIP-mediated alternative mRNA splicing fine-tunes the DNA damage response	6
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns	6
An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch	6
Antisense pairing and SNORD13 structure guide RNA cytidine acetylation	6
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs	6
No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA	6
CRED9: a differentially expressed elncRNA regulates expression of transcription factor CEBPA	6
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data	6
Generation of a newAdar1p150−/−mouse demonstrates isoform-specific roles in embryonic development and adult homeostasis	6
Differential translation of mRNA isoforms transcribed with distinct sigma factors	6
Identification and characterization of VapBC toxin–antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens	6
Pseudouridylation of Epstein-Barr virus noncoding RNA EBER2 facilitates lytic replication	6
Activity and substrate specificity of Candida, Aspergillus, and Coccidioides Tpt1: essential tRNA splicing enzymes and potential antifungal targets	6
Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease	6
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat	5
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection	5
Metal content and kinetic properties of yeast RNA lariat debranching enzyme Dbr1	5
T-hairpin structure found in the RNA element involved in piRNA biogenesis	5
Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination	5
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active	5
Applications and future of aptamers that achieve rapid-onset anticoagulation	5
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging	5
Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae	5
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae	5
SnoRNA guide activities: real and ambiguous	5
KRGG1 function in RNA editing inTrypanosoma brucei	5
A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix	5
µIVC-Useq: a microfluidic-assisted high-throughput functional screening in tandem with next-generation sequencing and artificial neural network to rapidly characterize RNA molecules	5
clipplotr—a comparative visualization and analysis tool for CLIP data	5
Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing	5
Exploring the targeting spectrum of rocaglates among eIF4A homologs	5
Drop-off-reinitiation at the amino termini of nascent peptides and its regulation by IF3, EF-G, and RRF	4
Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types	4
Far from home: the role of glial mRNA localization in synaptic plasticity	4
Biochemical and genetic dissection of the RNA-binding surface of the FinO domain ofEscherichia coliProQ	4
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	4
Understanding the redundant functions of the m6A-binding YTHDF proteins	4
Minimizing amplification bias during reverse transcription for in vitro selections	4
Consequences of depleting TNRC6, AGO, and DROSHA proteins on expression of microRNAs	4
Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability	4
Nanopore sequencing of internal 2′-PO4modifications installed by RNA repair	4
Alternative splicing regulation of membrane trafficking genes during myogenesis	4
IsoSplitter: identification and characterization of alternative splicing sites without a reference genome	4
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors	4
RNA in biological condensates	4
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs	4
Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium	4
Anionic G•U pairs in bacterial ribosomal rRNAs	4
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes	4
RNA:RNA interaction in ternary complexes resolved by chemical probing	4
RNA structure probing to characterize RNA–protein interactions on low abundance pre-mRNA in living cells	4
Molecular basis for GIGYF–TNRC6 complex assembly	4
Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions	4
A highly efficient human cell-free translation system	4
Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA–DNA adapter protein	4