RNA

Papers
(The median citation count of RNA is 3. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-07-01 to 2025-07-01.)
ArticleCitations
A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing101
Global profiling of the RNA and protein complexes ofEscherichia coliby size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)101
Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis83
Oppositional poly(A) tail length regulation by FMRP and CPEB179
Molecular basis for GIGYF–TNRC6 complex assembly76
Motifs in SARS-CoV-2 evolution72
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex167
Thg1 family 3′–5′ RNA polymerases as tools for targeted RNA synthesis58
Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging55
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 motor52
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors51
betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions51
Nuclear RNA-binding proteins meet cytoplasmic viruses46
NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-246
Optimized infrared photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells45
RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type45
The total mRNA concentration buffering system in yeast is global rather than gene-specific43
Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor41
Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering41
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription40
Small noncoding RNA interactome capture reveals pervasive, carbon source–dependent tRNA engagement of yeast glycolytic enzymes38
Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast35
Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria33
Far from home: the role of glial mRNA localization in synaptic plasticity30
3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations29
Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion29
The m6A-binding protein YTHDF3 modulates the cardiac response to stress28
A novel reporter for helicase activity in translation uncovers DDX3X interactions28
Exploring the targeting spectrum of rocaglates among eIF4A homologs25
A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication25
Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity25
Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF224
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements24
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story24
Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation24
Site-blocking antisense oligonucleotides as a mechanism to fine-tune MeCP2 expression24
Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations23
Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals23
Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function23
Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes23
Diversity and modularity of tyrosine-accepting tRNA-like structures23
Adenosine deaminases that act on RNA, then and now22
Corrigendum: Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores22
Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities22
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining22
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)21
Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing.20
clipplotr—a comparative visualization and analysis tool for CLIP data20
Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA20
Absolute Quantification of Mammalian MicroRNAs for Therapeutic RNA Cleavage and Detargeting20
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP20
Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes20
Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance20
Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNAIle(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA20
DDX3X and DDX3Y are redundant in protein synthesis20
Corrigendum: RNA partitioning into stress granules is based on the summation of multiple interactions20
Translation elongation inhibitors stabilize select short-lived transcripts19
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells19
The limits of human microRNA annotation have been met19
Localization of RNAs to the Mitochondria – Mechanisms and Functions19
Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA19
An incredible life in science: Joseph G. Gall (1928–2024)19
Boosting the toolbox for live imaging of translation18
The pseudotorsional space of RNA18
SMDesigner: a program to design sequence mutations to assess RNA structure18
Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs17
Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription17
The antivirulent Staphylococcal sRNA SprC regulates CzrB efflux pump to adapt its response to zinc toxicity17
RNA modifications: an overview of select web-based tools17
A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development17
Corrigendum: No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV, and MLV viral RNA17
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells16
EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53 mediated tumor suppression16
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 rRNA16
The catalytic-dead Pcif1 regulates gene expression and fertility inDrosophila16
Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation16
Double-stemmed and split structural variants of fluorescent RNA Mango aptamers16
Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF216
Chloroplast C-to-U RNA editing in vascular plants is adaptive due to its restorative effect: testing the restorative hypothesis15
Implications for OLE RNA as a natural integral membrane RNA15
Development of tailored splice-switching oligonucleotides for progressive brain disorders in Europe: development, regulation, and implementation considerations15
OpenASO: RNA Rescue — designing splice-modulating antisense oligonucleotides through community science15
SARS-CoV-2 infection triggers widespread host mRNA decay leading to an mRNA export block15
Functional analysis of the zinc finger modules of theSaccharomyces cerevisiaesplicing factor Luc715
Walter Keller (1938–2023): a tribute from his mentees14
The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode14
The daunting task of modifying ribosomal RNA14
Posttranscriptional modification to the core of tRNAs modulates translational misreading errors14
Corrigendum: NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal–ventral patterning14
Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations14
DNMT1 inhibition by pUG-fold quadruplex RNA14
Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex14
ac4C: a fragile modification with stabilizing functions in RNA metabolism14
Recoding UAG to selenocysteine inSaccharomyces cerevisiae14
The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns13
Conformational dynamics of the hepatitis C virus 3′X RNA13
RNA G-quadruplex structure targeting and imaging: recent advances and future directions13
Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p13
Global analysis by LC-MS/MS ofN6-methyladenosine and inosine in mRNA reveal complex incidence13
Corrigendum: Exploring the therapeutic potential of modulating nonsense-mediated mRNA decay13
Understanding the redundant functions of the m6A-binding YTHDF proteins13
Species-specific formation of paraspeckles in intestinal epithelium revealed by characterization of NEAT1 in naked mole-rat13
Microbial iCLIP2: enhanced mapping of RNA–protein interaction by promoting protein and RNA stability13
The molecular language of RNA 5′ ends: guardians of RNA identity and immunity12
Chemical manipulation of m1A mediates its detection in human tRNA12
Computational design and experimental verification of pseudoknotted ribozymes12
Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay12
Modulation of diverse biological processes by CPSF, the master regulator of mRNA 3′ ends12
Molecular basis of human polyA polymerase recruitment by mPSF11
Study of the RNA splicing kinetics via in vivo 5-EU labeling11
Alternative splicing regulation of membrane trafficking genes during myogenesis11
Analysis of programmed frameshifting during translation ofprfBinFlavobacterium johnsoniae11
KRGG1 function in RNA editing inTrypanosoma brucei11
The unfolding landscape of RNA and disease11
The essential role of architectural noncoding RNANeat1in cold-induced beige adipocyte differentiation in mice11
How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active11
The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets, by Thomas R. Cech. 2024. W.W. Norton & Company11
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function11
Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs11
RNA gain-of-function mechanisms in short tandem repeat diseases10
Cytoplasmic regulation of the poly(A) tail length as a potential therapeutic target10
Autorecoding A-to-I RNA editing sites in theAdargene underwent compensatory gains and losses in major insect clades10
Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast10
Cross-linking mass spectrometric analysis of the endogenous TREX complex fromSaccharomyces cerevisiae10
Targeting splicing factors for cancer therapy10
Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis10
SnoRNA guide activities: real and ambiguous10
Nanopore-based RNA sequencing deciphers the formation, processing, and modification steps of rRNA intermediates in archaea10
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes10
Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server10
Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs10
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA10
RNA sequence and structure control assembly and function of RNA condensates10
Rational design yields RNA-binding zinc finger domains with altered sequence specificity10
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of theBDF2mRNA9
Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development9
The life and times of a tRNA9
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3′-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides9
m6A-ELISA, a simple method for quantifyingN6-methyladenosine from mRNA populations9
T1TAdb: the database of type I toxin–antitoxin systems9
Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor inSaccharomyces cerevisiae9
Theje ne sais quoiof 5-methylcytosine in messenger RNA9
The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression9
Antisense modulation of IL7R splicing to control sIL7R expression in human CD4+T cells9
RNA aptamers as tools for the purification and analysis of in vivo assembled Ribonucleoproteins9
Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders9
TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome9
Tribute to Yoshiro Shimura (1932–2023)9
Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging9
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures8
Is there a localized role for translational quality control?8
Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E8
i-tRAP (individual tRNA acylation PCR): a convenient method for selective quantification of tRNA charging8
Quantification of tRNA m1A modification by templated-ligation qPCR8
On the origin of life: an RNA-focused synthesis and narrative8
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease8
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA8
SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells8
Crystal structures of free-state tRNALeu reveal conformational flexibility of Type-II tRNAs8
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing8
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data8
The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements8
Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line8
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast8
Design considerations for analyzing protein translation regulation by condensates8
Two dynamic N-terminal regions are required for function in ribosomal RNA adenine dimethylase family members8
Alu RNA pseudoknot alterations influence SRP9/SRP14 association8
Robo-Therm, a pipeline to RNA Thermometer discovery and validation8
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq8
Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development8
Examining SRP pathway function in mRNA localization to the endoplasmic reticulum8
Human T-cell leukemia virus type 1 uses a specific tRNAProisodecoder to prime reverse transcription8
Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes7
Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF7
Dissecting the stress granule RNA world: dynamics, strategies, and data7
Structural analysis of MALAT1 long noncoding RNA in cells and in evolution7
RNA therapeutics7
A crescendo of competent coding (c3) contains the Standard Genetic Code7
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding7
Recollections: Yasuhiro Furuichi (1940–2022)7
A Role for SNU66 in Maintaining 5’ Splice Site Identity During Spliceosome Assembly7
Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments7
2′-O-methylation (Nm) in RNA: progress, challenges, and future directions7
Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation7
RNA in biological condensates7
Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis7
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing inC. elegans6
Vault RNA1–1 riboregulates the autophagic function of p62 by binding to lysine 7 and arginine 21, both of which are critical for p62 oligomerization6
The universally conserved nucleotides of the small subunit ribosomal RNAs6
Thermodynamic control of mismatch discrimination for extensive splicing regulation of PKM pre-mRNA6
A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly6
In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans6
Distinct Gag interaction properties of HIV-1 RNA 5′ leader conformers reveal a mechanism for dimeric genome selection6
Artifacts and biases of the reverse transcription reaction in RNA sequencing6
Fungi of the order Mucorales express a “sealing-only” tRNA ligase6
Corrigendum: Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells6
Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance6
Corrigendum: Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity6
FLAME: long-read bioinformatics tool for comprehensive spliceome characterization6
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures6
Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling6
A general and biomedical perspective of viral quasispecies6
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules6
Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts6
Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression5
Principles, functions, and biological implications of m6A in plants5
The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes5
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 yeasts5
NMDtxDB: data-driven identification and annotation of human NMD target transcripts5
How do protein domains of low sequence complexity work?5
Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes inTrypanosoma brucei5
Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides5
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-435
Anionic G•U pairs in bacterial ribosomal rRNAs5
Challenges to mapping and defining m6A function in viral RNA5
FISH-quant v2: a scalable and modular tool for smFISH image analysis5
Biochemical characterization of mRNA capping enzyme from Faustovirus5
TheEscherichia coli ribBriboswitch senses flavin mononucleotide within a defined transcriptional window5
Expansion and functional analysis of the SR-related protein family across the domains of life5
Development, validation, and application of the ribosome separation and reconstitution system for protein translation in vitro5
Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing5
lncRNA BC200 is processed into a stable Alu monomer5
Principles, mechanisms, and biological implications of translation termination–reinitiation5
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex5
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA5
Corrigendum: Identification of Up47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium5
DRBD18 acts as a transcript-specific RNA editing auxiliary factor inTrypanosoma brucei5
A general RNA-templated RNA extension activity of E. coli RNA polymerase5
RNase L produces tRNA-derived RNAs that contribute to translation inhibition5
Z-RNA biology: a central role in the innate immune response?5
Sod1-deficient cells are impaired in formation of the modified nucleosides mcm5s2U and yW in tRNA5
tRNATyrhas an unusually short half-life inTrypanosoma brucei5
Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing5
Structures of RNA ligase RtcB in complexes with divalent cations and GTP5
Nanopore sequencing of RNA and cDNA molecules in Escherichia coli4
RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits inStaphylococcus aureus4
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 compositions4
RNA-binding proteins in disease etiology: fragile X syndrome and spinal muscular atrophy4
Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism4
Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation4
Identification of leader–trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea4
lncRNAMalat1and miR-26 cooperate in the regulation of neuronal progenitor cell proliferation and differentiation4
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing4
Beyond RNA-binding domains: determinants of protein–RNA binding4
Translational control byTrypanosoma bruceiDRBD18 contributes to the maintenance of the procyclic state4
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection4
Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets4
The kinesin motor KIF1C is a putative transporter of the exon junction complex in neuronal cells4
Which came first: the chicken, the egg, or guanine?4
tRNA-like leader-trailer interaction promotes 3′-end maturation of MALAT14
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