The official journal of the RNA Society. Featuring cutting edge research in RNA Biology, biochemistry, genetics, cell biology, structural biology and genomics
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Nanopore direct RNA sequencing is redefining how we detect RNA modifications, enabling long-read, transcriptome-wide views with minimal RNA handling. This perspective highlights both the power and current limitations of DRS in probing the epitranscriptome bit.ly/4dx1lec
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How well can machine learning predict RNA secondary structure? This review surveys current approaches—from deep learning to hybrid models—highlighting both impressive gains and key limitations in generalizability and interpretability bit.ly/4spSj6s
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What does it mean to study RNA at system scale? This Special Issue perspective lays out a roadmap—from quantitative transcriptomics to integrative modeling—defining how we measure, model, and ultimately manipulate RNA across biological systems bit.ly/3POaGo9
#RNAbiology
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Excited to highlight the new Special Issue of RNA showcasing advances in system-level RNA biology, from epitranscriptomics and RNA damage to deep learning–driven structure prediction and beyond. A strong snapshot of where the field is heading bit.ly/4tEQL9I
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Two amino acids in each homologous PUF repeat make molecular contacts that drive base recognition. These molecular contacts cannot generally be functionally interchanged between repeats, as shown bit.ly/3OrhTtq
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The proteome is dynamically remodeled across the mammalian cell cycle. Here, we review the mechanistic basis and functional consequences of cell cycle-specific mRNA decay and translational control bit.ly/4atoJYd
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Translation elongation stresses like tRNA synthetase inhibitors induce the stress response but inhibit translation elongation, leading to a parabolic dose-response pattern of stress granule assembly bit.ly/4aANDUi
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Complementary DNA oligonucleotide direct in-gel quantification (cDINGQ) for precise tRNA fragment analysis bit.ly/3ZEmn2g
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In the cytoplasm of neuroblastoma cells, PTBP1 maintains CyCoNP homeostasis by modulating miR-4492 loading, sustaining NCAM1 expression. PTBP1 loss enhances miRNA repression over CyCoNP. #lncRNA bit.ly/3Mrgx1k
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eRNAs extend enhancer function beyond transcription. Mapping eRNA decay reveals cytoplasmic eRNAs stabilise mRNAs and boost translation, helping enhancers finish the job they start bit.ly/4rXB9NU
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MiSiPi.RNA is a software package written in R for the classification of animal small RNAs into major known types: microRNAs (mi), small-interfering RNAs (si), and piwi-interacting RNAs (pi). This comprehensive tool calculates over 20 parameters bit.ly/4cwTxIJ
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Prime positions in sRNA binding sites located in coding sequences are adjusted with the reading frame and often coincide with the most frequent codons bit.ly/4aHTd7I
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Telomeres are transcribed into TERRA. We showed that iTERRA is transcribed from interstitial telomeric repeats (ITSs) and that CpG island subtelomeric promoters are also present at interstitial sites bit.ly/4oD0UBH
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Mutation of a conserved amino acid in the Prp8 alpha-finger increases use of non-YAG 3' splice sites in budding yeast and provides insight into Prp22 ATPase function. bit.ly/47YRb1g
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m⁵C-Rol-LAMP, a simple qPCR-based assay, quantifies m⁵C RNA methylation at single nucleotides and uncovers stress-regulated rRNA modification in bacteria. bit.ly/43AWnr4 #LMU_muenchen #lifescimunich #RNA #CRC1309
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Conserved protein Seb1 that interacts with RNA polymerase II and RNA is an anti-pausing transcription elongation factor bit.ly/4pbUQzQ
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IsoformMapper creates protein networks from AlphaFold models and uses InfoMap community detection to compare isoform structures and visualize alternative splicing consequences via alluvial diagrams. bit.ly/49n4USa #AlternativeSplicing #RNASplicing
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A genome-wide screen revealed that proteins lacking stable structures can be just as essential as folded ones. Among them, FAM32A plays a crucial role in RNA splicing. @UTokyo_News_en @KotaroTsuboyama bit.ly/4o7muy3
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A PLP-RCA method enables simultaneous, in situ detection of AAV transgene DNA and mRNA at single-cell resolution, enabling the analysis of genome processing and transduction efficiency. bit.ly/4qoAR2g
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By analyzing the subcellular localization of various UPF1 mutants, we show that UPF1’s nuclear-cytoplasmic shuttling is independent of its ATPase and RNA binding activities, with RNA binding itself being a key determinant of its cytoplasmic retention. bit.ly/3IFlQII
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Molecular dynamics reveal how Mg²⁺, K⁺ and Gdm⁺ synergistically drive allosteric changes in the ykkC-I riboswitch aptamer, fine-tuning the RNA conformational landscape for function. bit.ly/4hgs9ze
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NMR structures and ³J couplings combined with MD and maximum entropy refinement yield ensembles consistent with experiment, revealing dynamic conformations of Omicron s2m RNA. bit.ly/4nUTycB
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DEAD-box protein Prp5 hydrolyzes ATP/ATPγS to drive prespliceosome formation. ATP is dispensable in the absence of Sub2, which is not essential, but facilitates splicing by stabilizing Msl5 binding. bit.ly/4nw3sB3
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SpDis3L2-U13 RNA crystal structure further unveils its degradation mechanism. A single substitution at A756 disrupts Dis3L2’s ability to process structured RNAs, highlighting a key functional residue. bit.ly/4pTuJyO
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Tiny ocean creatures called diplonemids bend the rules of genetics! Their genes are packed with unusual introns, yet their editing system works fine, showing the flexibility of life. bit.ly/3KUBOPC
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This work highlights the conserved role of NMD in the degradation of lncRNAs in an RNAi-capable budding yeast and provides insight into the functional impact of endogenous RNAi on the transcriptome. bit.ly/3IvOmwj
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Crystal structure of the LIG-KIN domains of fungal tRNA ligase Trl1 reveals interdomain assembly and RNA transfer model, offering insight into a possible antifungal target. bit.ly/3IZ7SBn
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Loss of a base (A3027) in the sarcin/ricin loop (PDB 4V7R) of 25S rRNA is sensed by factors detecting slow-moving ribosomes. Ubiquitination of the small subunit occurs, despite large subunit damage. bit.ly/4pRJfHD
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Desthiobiotin (DTB)-modified and TAMRA-modified 2''OMeNAD+ are RNA 2'-phosphotransferase (Tpt1) poisons that enable affinity-tagging and fluorescence-tagging of internal RNA 2'-phosphate groups. bit.ly/46dMUHZ
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The #RNA editing enzyme ADAR1 is an important target for many cancers. This study evaluated ZYS-1, a recently reported ADAR1 inhibitor, and found no evidence supporting ZYS-1 as an ADAR1 inhibitor. bit.ly/4nEK7xc
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T-box-i is a novel, effective inhibitor of T-box riboswitches with antimicrobial activity against Staphylococcus aureus. bit.ly/4nyMmSE
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HPV E6 exploits codon usage to reduce antigen presentation and evade immunity; combinations of synonymous substitutions restore E6 expression and T cell activation. bit.ly/3VUKzvo
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HRV-B3 IRES acts as a position-dependent negative regulator of RNA abundance from the upstream promoter. We found that this effect can be mitigated by inserting a spacer between IRES and the promoter. bit.ly/4nEhYGA
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Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery. bit.ly/4n38pB3
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CSDE1 is present at low levels in healthy melanocytes, but upon transformation its expression rises and it becomes phosphorylated, promoting stronger interactions with ribosomes, possibly at membrane. bit.ly/3JOdi2c
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TRAP1 moonlights as an RNA-binding protein, enhancing translation of the splicing factor LUC7L3 to drive proliferation in high-grade serous ovarian cancer cells. #TRAP1 #RBP #ovariancancer @rusiario bit.ly/47t3apu
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OMA-1 is a zinc finger RNA-binding protein required for oocyte maturation. This work identifies an arginine-rich peptide upstream of the zinc finger required for both RNA binding and embryogenesis. bit.ly/3JBkwXg
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The absence of an inductive effect confers pseudouridine residues with resistance to enzyme-catalyzed and spontaneous strand cleavage. bit.ly/4lF0dFP
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PACT suppresses PKR activation, thus preventing activation of the integrated stress response, NF-κB, and cell death. Dimerization and double-stranded #RNA binding by PACT is required for this function. bit.ly/4oC3Vm7 @KyleCottrell @PurdueBiochem @PUCancerInst
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Spatiotemporal NAIL-MS analysis shows that ALKBH5 does not affect global m6A turnover in human mRNA across subcellular compartments under standard growth conditions. bit.ly/4lvVtC6
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An internal 8U tract in a recoded influenza A virus segment causes viral polymerase slippage. This in turn leads to truncated protein production, interferon stimulation and reduced virus production. bit.ly/4lr9hxX
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FBF-1 RNA binding is not regulated by its C-terminal tail (CT), whereas highly similar FBF-2 is inhibited by its essential CT. Partner protein competes with CT binding to regulate FBF-2 but not FBF-1. bit.ly/3UjicGr
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We present a method to profile RNA within membrane-less organelles, utilizing in situ transcription and linear amplification. We substantiate the accumulation of immature pre-mRNAs in stress granules. bit.ly/4mALAEk
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Two-step VEGF HDB recognition by an aptamer, t44.27, was unveiled. Transient interaction was followed by a tight-complex formation and latter of which is essential to antagonize heparin binding. bit.ly/4lb8Uap
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Coevolution of protein-only RNase P and tRNA genes in Aquifex aeolicus: most precursor tRNAs have an A residue upstream of the 5’-cleavage site and generally lack stable acceptor stem extensions. bit.ly/4m4oKF0
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In silico λ-dynamics accurately predicts interactions of modified RNA to a model RNA-binding protein. The work opens opportunities to study modified RNA-protein interactions without in vitro reagents. bit.ly/45v1nO3
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Translational helicases eIF4A, Ded1 and Slh1 are found to be dispensable for mRNA scanning in search of the start codon by 40S ribosomes. Instead, mRNA scanning is driven by one-dimensional diffusion. bit.ly/4mxiYeY
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Visualization of full-length 7SK and 7SL RNAs tertiary atomistic models derived using small-angle x-ray scattering, coarse-grained modelling, and molecular dynamics simulations. bit.ly/45pKe8e
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Stress granules elevate p21 RNA levels and reduce Rb phosphorylation, promoting cell cycle exit. bit.ly/46IvJ1P
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Rampant A-to-I RNA editing in Drosophila lncRNA roX1 is non-adaptive and does not provide a selective advantage to the organism. bit.ly/45a2C6p
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Eukaryotic translation initiation factors (eIFs) 5 and 2B compete for eIF2. The three binding sites on eIF2β (K1, K2, and K3) allow simultaneous binding and faster mutual displacement from eIF2γ. bit.ly/4lgdcgE
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