RNA

Article	Citations
Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection	400
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols	209
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look	185
Aminoacyl-tRNA synthetases	179
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers	97
The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation	96
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block	62
The emerging structural complexity of G-quadruplex RNAs	56
RNA partitioning into stress granules is based on the summation of multiple interactions	55
RNA in formation and regulation of transcriptional condensates	52
FISH-quant v2: a scalable and modular tool for smFISH image analysis	39
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance	38
DDX3X and DDX3Y are redundant in protein synthesis	36
The virtual circular genome model for primordial RNA replication	36
Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads	36
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli	35
Sensing of transposable elements by the antiviral innate immune system	34
Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes	33
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome	32
Phosphodiester modifications in mRNA poly(A) tail prevent deadenylation without compromising protein expression	32
Long noncoding RNA and protein abundance in lncRNPs	31
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein	31
Cyclic oligoadenylate signaling and regulation by ring nucleases during type III CRISPR defense	30
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression	29
Are stress granules the RNA analogs of misfolded protein aggregates?	29

YTHDF2 destabilizes m6A-modified neural-specific RNAs to restrain differentiation in induced pluripotent stem cells	29
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein	29
Nuclease-mediated depletion biases in ribosome footprint profiling libraries	28
Circulating SNORD57 rather than piR-54265 is a promising biomarker for colorectal cancer: common pitfalls in the study of somatic piRNAs in cancer	28
How do protein domains of low sequence complexity work?	27
Elimination of Calm1 long 3′-UTR mRNA isoform by CRISPR–Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice	27
RNA multimerization as an organizing force for liquid–liquid phase separation	26
Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA	26
The life and times of a tRNA	25
Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA	25
5′ tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene expression	25
Viral subversion of nonsense-mediated mRNA decay	25
Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot	24
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea	24
A mark of disease: how mRNA modifications shape genetic and acquired pathologies	24
Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules	23
Physiologic RNA targets and refined sequence specificity of coronavirus EndoU	23
Rampant C-to-U deamination accounts for the intrinsically high mutation rate in SARS-CoV-2 spike gene	23
A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation	23
Argonaute binding within human nuclear RNA and its impact on alternative splicing	23
Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch	23
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly	22
Nuage condensates: accelerators or circuit breakers for sRNA silencing pathways?	21
Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes	21
A second riboswitch class for the enzyme cofactor NAD+	21
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions	21
Cold-inducible RNA binding protein promotes breast cancer cell malignancy by regulating Cystatin C levels	20
Studies with recombinant U7 snRNP demonstrate that CPSF73 is both an endonuclease and a 5′–3′ exonuclease	20
Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent	20
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET	20
What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?	20
Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6	19
A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs	19
Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing	19
An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7	19
A model for DHX15 mediated disassembly of A-complex spliceosomes	18
The limits of human microRNA annotation have been met	18
Validation strategies for antibodies targeting modified ribonucleotides	18
Exploring the epitranscriptome by native RNA sequencing	18
5-methylcytosine modification of an Epstein–Barr virus noncoding RNA decreases its stability	17
RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes	17
mRNA spindle localization and mitotic translational regulation by CPEB1 and CPEB4	17
Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation	17
Requirement for cleavage factor IIm in the control of alternative polyadenylation in breast cancer cells	17
Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides	16
Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy	16
Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning	16
The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2′-O-Me sites	16
Using quantitative reconstitution to investigate multicomponent condensates	16
PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells	16

Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation	16
Muscleblind-like 2 controls the hypoxia response of cancer cells	16
Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA	15
Revisiting tRNA chaperones: new players in an ancient game	15
Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem?	15
A robust and versatile method for production and purification of large-scale RNA samples for structural biology	15
Pathological phase transitions in ALS-FTD impair dynamic RNA–protein granules	15
Ribosome profiling reveals novel regulation of C9ORF72 GGGGCC repeat-containing RNA translation	15
Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin	15
microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs	15
2′-fluoro-modified pyrimidines enhance affinity of RNA oligonucleotides to HIV-1 reverse transcriptase	15
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses	15
Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder	15
Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation	15
Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae	15
Ensemble switching unveils a kinetic rheostat mechanism of the eukaryotic thiamine pyrophosphate riboswitch	15
Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly	15
Splicing conservation signals in plant long noncoding RNAs	15
Specificity in the biosynthesis of the universal tRNA nucleoside N6-threonylcarbamoyl adenosine (t6A)—TsaD is the gatekeeper	14
Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation	14
In vitro studies provide insight into effects of Dicer-2 helicase mutations inDrosophila melanogaster	14
Structure of 3′-PO4/5′-OH RNA ligase RtcB in complex with a 5′-OH oligonucleotide	14
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations	14
Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis	14
Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome	14
RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing	14
A combinatorially regulated RNA splicing signature predicts breast cancer EMT states and patient survival	14
tRNA elbow modifications affect the tRNA pseudouridine synthase TruB and the methyltransferase TrmA	14
Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis	14
Cotranscriptional splicing efficiencies differ within genes and between cell types	14
The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold	13
A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor	13
Fusion protein EWS-FLI1 is incorporated into a protein granule in cells	13
The role of stress-activated RNA–protein granules in surviving adversity	13
An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano	13
PDCD4 regulates axonal growth by translational repression of neurite growth-related genes and is modulated during nerve injury responses	13
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays	13
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique	13
Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels	13
Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels	13
RNase H-based analysis of synthetic mRNA 5′ cap incorporation	12
Human disease-associated single nucleotide polymorphism changes the orientation of DROSHA on pri-mir-146a	12
Evaluating DCA-based method performances for RNA contact prediction by a well-curated data set	12
Termi-Luc: a versatile assay to monitor full-protein release from ribosomes	12
A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data	12
Highly specific, multiplexed isothermal pathogen detection with fluorescent aptamer readout	12
RNA sequence and structure control assembly and function of RNA condensates	12
Deflating the RNA Mg2+ bubble: stereochemistry to the rescue!	12
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis	12
Frameshifting at collided ribosomes is modulated by elongation factor eEF3 and by integrated stress response regulators Gcn1 and Gcn20	12
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores	12
Mutations in domain IV of elongation factor EF-G confer −1 frameshifting	12
Folding heterogeneity in the essential human telomerase RNA three-way junction	12
T1TAdb: the database of type I toxin–antitoxin systems	11
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments	11
HIV-1 spliced RNAs display transcription start site bias	11
Pdc2/Pat1 increases the range of decay factors and RNA bound by the Lsm1–7 complex	11
An ancient evolutionary connection between Ribonuclease A and EndoU families	11
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing	11
Widespread genetic heterogeneity of human ribosomal RNA genes	11
Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)	11
Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon	11
The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication	11
The total mRNA concentration buffering system in yeast is global rather than gene-specific	11
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development	11
The stem cell–specific protein TRIM71 inhibits maturation and activity of the prodifferentiation miRNA let-7 via two independent molecular mechanisms	11
DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells	11
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	10
Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates	10
Adaptor protein RapZ activates endoribonuclease RNase E by protein–protein interaction to cleave a small regulatory RNA	10
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions	10
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization	10
Mitochondrial misreading in skeletal muscle accelerates metabolic aging and confers lipid accumulation and increased inflammation	10
Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion	10
Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics	10
Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-MIRHG for efficient cell cycle reentry	10
Single-cell transcriptome sequencing on the Nanopore platform with ScNapBar	10
Validation and classification of RNA binding proteins identified by mRNA interactome capture	10
RNALigands: a database and web server for RNA–ligand interactions	10
Transcription and splicing dynamics during early Drosophila development	10

Human spliceosomal snRNA sequence variants generate variant spliceosomes	10
Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses	10
SRSF10: an atypical splicing regulator with critical roles in stress response, organ development, and viral replication	10
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing	10
Processing ofAlusmall RNAs by DICER/ADAR1 complexes and their RNAi targets	9
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	9
Single-pass transcription by T7 RNA polymerase	9
Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes	9
Solution structure and RNA-binding of a minimal ProQ-homolog fromLegionella pneumophila(Lpp1663)	9
Dynamic association of human Ebp1 with the ribosome	9
Acyclic (S)-glycol nucleic acid (S-GNA) modification of siRNAs improves the safety of RNAi therapeutics while maintaining potency	9
Z-RNA biology: a central role in the innate immune response?	9
Dual-level autoregulation of the E. coli DeaD RNA helicase via mRNA stability and Rho-dependent transcription termination	9
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing	9
Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline	9
Global SLAM-seq for accurate mRNA decay determination and identification of NMD targets	9
Roadblock-qPCR: a simple and inexpensive strategy for targeted measurements of mRNA stability	9
Review of single-cell RNA-seq data clustering for cell-type identification and characterization	8
Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation	8
RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands	8
Evolutionary divergence of Firre localization and expression	8
Posttranscriptional modifications at the 37th position in the anticodon stem–loop of tRNA: structural insights from MD simulations	8
The landscape of translational stall sites in bacteria revealed by monosome and disome profiling	8
3′READS + RIP defines differential Staufen1 binding to alternative 3′UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association	8
VfoldMCPX: predicting multistrand RNA complexes	8
RNAi in cell nuclei: potential for a new layer of biological regulation and a new strategy for therapeutic discovery	8
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease	8
siRNA potency enhancement via chemical modifications of nucleotide bases at the 5′-end of the siRNA guide strand	8
Annotation of the local context of RNA secondary structure improves the classification and prediction of A-minors	8
Influenza A virus utilizes noncanonical cap-snatching to diversify its mRNA/ncRNA	8
Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase	8
Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery	8
Saccharomyces cerevisiae Ecm2 modulates the catalytic steps of pre-mRNA splicing	8
Disease-associated mutations in mitochondrial precursor tRNAs affect binding, m1R9 methylation, and tRNA processing by mtRNase P	8
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type	8
RNA secondary structures in Dscam1 mutually exclusive splicing: unique evolutionary signature from the midge	8
Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts	8
Expansion segments in bacterial and archaeal 5S ribosomal RNAs	8
Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein–protein intersubunit bridge B1b	7
The ribosome epitranscriptome: inert—or a platform for functional plasticity?	7
N2 modified dinucleotide cap analogs as a potent tool for mRNA engineering	7
Expansion and functional analysis of the SR-related protein family across the domains of life	7
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story	7
Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA	7
Transcriptional profiling of fission yeast RNA polymerase II CTD mutants	7
A survey of RNA editing at single-cell resolution links interneurons to schizophrenia and autism	7
Structure of the dengue virus RNA promoter	7
U2AF2 binds IL7R exon 6 ectopically and represses its inclusion	7
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication	7
Biological solution conditions and flanking sequence modulate LLPS of RNA G-quadruplex structures	7
Type III-A CRISPR systems as a versatile gene knockdown technology	7
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	7
KDM3A regulates alternative splicing of cell-cycle genes following DNA damage	6
Transcription-dependent enrichment of the yeast FACT complex influences nucleosome dynamics on the RNA polymerase III-transcribed genes	6
Functional regions in the 5′ external transcribed spacer of yeast pre-rRNA	6
The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation	6
The universally conserved nucleotides of the small subunit ribosomal RNAs	6
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs	6
Mechanistic analysis of the enhanced RNAi activity by 6-mCEPh-purine at the 5′ end of the siRNA guide strand	6
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)	6
OTTER, a new method for quantifying absolute amounts of tRNAs	6
Unusual tertiary pairs in eukaryotic tRNAAla	6
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	6
Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis	6
The RNA transport factor PHAX is required for proper histone H2AX expression and DNA damage response	6
Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus	6
Targeting splicing factors for cancer therapy	6
Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand	6
Oppositional poly(A) tail length regulation by FMRP and CPEB1	6
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	6
Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments	6
Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination	6
ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations	6
Ancient microRNA profiles of 14,300-yr-old canid samples confirm taxonomic origin and provide glimpses into tissue-specific gene regulation from the Pleistocene	6
The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase binding in 40S ribosome assembly	6
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades	6
Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities	6
Human RNase P: overview of a ribonuclease of interrelated molecular networks and gene-targeting systems	6
DNMT1 inhibition by pUG-fold quadruplex RNA	6
Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei	6
Future directions for medicinal chemistry in the field of oligonucleotide therapeutics	6
ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5′ splice site motifs within nuclear speckles	5
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes	5
CtIP-mediated alternative mRNA splicing fine-tunes the DNA damage response	5
Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inBacillus subtilis	5
RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells	5
Structures of RNA ligase RtcB in complexes with divalent cations and GTP	5
A rare bacterial RNA motif is implicated in the regulation of thepurFgene whose encoded enzyme synthesizes phosphoribosylamine	5
Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease	5
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals	5
Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing	5
A versatile tRNA modification-sensitive northern blot method with enhanced performance	5
CRED9: a differentially expressed elncRNA regulates expression of transcription factor CEBPA	5
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay	5
Sulfonated inhibitors of the RNA editing ligases validate the essential role of the MRP1/2 proteins in kinetoplastid RNA editing	5