What’s next for RNA biology at system scale? This editorial frames a shift toward quantitative, integrative approaches, highlighting advances in measuring, modeling, and manipulating RNA across biological systems #RNAbiology #SystemsBiology #Genomics #RNAseq #ComputationalBiology bit.ly/41hv9UJ

RNA doesn’t just encode information, it helps build cellular structure. This review explores how RNAs drive the formation of biomolecular condensates, shaping organization, regulation, and function across contexts #RNAbiology #PhaseSeparation #BiomolecularCondensates #CellBiology bit.ly/4mjjI8B

RNA isn’t just regulated in time—it’s regulated in space. This review explores mechanisms of mRNA localization and localized translation, highlighting how spatial control shapes cellular function and specialization #RNAbiology #mRNAlocalization #GeneRegulation #CellBiology #RNAseq bit.ly/4eboUJF

How do we connect RNA structure to function? This review highlights new approaches to probe RNA structure across dimensions, linking structural features to RNA activity, interactions, and regulation in complex cellular contexts #RNAbiology #RNAstructure #Genomics #ComputationalBiology bit.ly/4sthgOt

Can we drug RNA? This review explores the landscape of RNA-targeting small molecules, highlighting strategies to identify binding sites, design ligands, and overcome challenges posed by RNA structural flexibility #RNAbiology #RNAstructure #ChemicalBiology #DrugDiscovery #Genomics bit.ly/4sv5Dq1

RNA function is defined by its interactions. This review surveys cutting-edge methods to map protein–RNA and RNA–RNA contacts, outlining how we can now begin to reconstruct RNA interaction networks at transcriptome scale #RNAbiology #Interactome #RNAprotein #Genomics #SystemsBiology bit.ly/41KDfWl

How well can machine learning predict RNA secondary structure? This review surveys current approaches highlighting both impressive gains and key limitations in generalizability and interpretability #RNAbiology #MachineLearning #RNAstructure #ComputationalBiology #Genomics bit.ly/4spSj6s

Nanopore direct RNA sequencing is redefining how we detect RNA modifications and damage—enabling long-read, transcriptome-wide views with minimal RNA handling. This perspective highlights DRS in probing the epitranscriptome #RNAbiology #Epitranscriptomics #Nanopore #RNAseq #Genomics bit.ly/4dx1lec

What does it mean to study RNA at system scale? This perspective lays out a roadmap—from quantitative transcriptomics to integrative modeling—for how we measure, model, and ultimately manipulate RNA across biological systems #RNAbiology #SystemsBiology #Genomics #ComputationalBiology bit.ly/3POaGo9

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 #RNAbiology #Epitranscriptomics #RNAseq #ComputationalBiology #Genomics bit.ly/4tEQL9I

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

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

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

Complementary DNA oligonucleotide direct in-gel quantification (cDINGQ) for precise tRNA fragment analysis bit.ly/3ZEmn2g

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

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

Modulating the cleavage and polyadenylation site: from research tools to therapeutic opportunities #RNAbiology #CRISPR bit.ly/4cwUlxf

MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing bit.ly/4cwTxIJ

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

ML for RNA secondary structure: Review of field's evolution from classical methods to DL and foundation models. Explores data evolution, the generalization crisis, struggles, and perspectives #RNA #DeepLearning bit.ly/4az24YW

The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD bit.ly/40gO8Ow

Segar et al. explore the diversity and distribution of a type of Internal Ribosome Entry Site (IRES) RNA, uncovering examples that may reveal mechanistic variation and host species adaptation bit.ly/3OhYlaW

The DDX3X inhibitor, RK-33, induces stress granules via the integrated stress response and inhibits the proliferation of the human coronavirus OC43 in a manner independent of DDX3X @checht6.bsky.social @colorado.edu @hhmi-science.bsky.social bit.ly/3MfTJ4C

This work dissects a segment of insulin receptor mRNA with structure and function experiments, revealing necessary and sufficient elements that promote robust translation under stress bit.ly/4aRIbxH

G4-stabilizing and -destabilizing ligands suppress PDCoV proliferation by targeting PDCoV-G4, highlighting the importance of optimal G4 stability for PDCoV and its potential as an antiviral target bit.ly/4tCkFvV

SFPQ maintains paraspeckle independence by preventing their engulfment by nuclear speckles, via accumulation of its blocky P/Q-patterned IDR within the paraspeckle shell bit.ly/3OaCZwh

T7 RNAP-generated transcripts produce double-stranded RNA byproducts that trigger formation of PKR-dependent stress granules. Uridine analogues block production of dsRNA. At high concentrations, RNA free of ds byproducts triggers formation of PKR-independent stress granules bit.ly/4riqTiZ

Advances in CLIP-derived methods have enabled high-resolution mapping of individual RNA binding protein-RNA interactions as well as RNA binding protein-associated RNA–RNA interactions #RNA #CLIP @evannostrandlab.bsky.social bit.ly/4bYjAsg

We use a newly curated benchmark dataset to show that the limited diversity of known RNA structures impacts deep learning methods’ performance on structures different from seen data bit.ly/4qWoTfL

In this review we highlight how bridging single-molecule imaging and genome-wide Ribo-Seq experiments can shed light on complex mRNA translation dynamics across scales. #Translation #RiboSeq @tim-stasevich.bsky.social bit.ly/3LQ08Dc

RNA contains only one functional group that can donate two H-bonds: the exocyclic amine. We reveal how this dual-donating capacity plays key roles in diverse RNA structural motifs and functional RNAs bit.ly/3Nx1SS8

A Mycobacterium tuberculosis Mbox controls a conserved, small upstream ORF via a translational expression platform and rho-dependent termination of transcription bit.ly/4qbzPX4

Genome-wide comparison of all known pestiviruses uncovers conserved known and novel RNA secondary structures. #Pestivirus #RNA #alignment bit.ly/4qL3nuF

Galbraith et al from #Dalhousie University Department of Microbiology & Immunology show that the lack of guanosines 10-18 nt downstream from the 5’ cap makes mRNAs resistant to SARS-CoV2 Nsp1 shutoff bit.ly/3LaucZX

Nanopore direct RNA sequencing is now accurate enough to provide insightful new information about epitranscriptomic modifications as well as RNA damage arising from cellular stress bit.ly/49uRHGD

A review on representation learning of single-cell RNA-seq data by Constantin Ahlmann-Eltze (@const-ae.bsky.social), Florian Barkmann (@flobarkmann.bsky.social), Jan Lause (@janlause.bsky.social), Valentina Boeva (@valboeva.bsky.social), and Dmitry Kobak (@hippopedoid.bsky.social) bit.ly/49vWRSJ

High-stoichiometry m6A sites are evolutionarily conserved bit.ly/498rOuQ

In this review, we highlight the recent innovations that have expanded the utility of ribosome profiling (Ribo-seq) to resolve distinct ribosome populations, and how these approaches advanced our understanding of translational control bit.ly/4p4aY6h

AGO–small RNA loading specificity arises from the integration of structural and biochemical features together with the spatiotemporal co-localization of small RNAs and their Argonaute partners bit.ly/48TOrnW

SF3B1K700E rewires splicing of cell-cycle regulators bit.ly/4sq6eKP

Mapping 5’ and 3’ ends of poly(A)-enriched RNA in the fungal pathogen Aspergillus fumigatus reveals the first evidence of promoter-proximal premature transcriptional termination in the Eurotiomycetes bit.ly/3MnImHp

PANTHER score, a ML-based scoring function model, opens the door to faster, more interpretable, and more cost-effective predictions of protein-RNA binding affinity #Exscalate #RNA #RNATherapeutics @unimont.bsky.social bit.ly/3Kkd97r

5' UTR cis-features play a central role in ribosome engagement on coding and noncoding RNAs. Feature architectures relate to efficient long-UTR mRNA translation and nonproductive ncRNA binding bit.ly/4poRtq3

MUTACLASH maps functional small RNA–target interactions through crosslinking-induced mutations, uncovering biologically relevant miRNA and piRNA targeting sites in CLASH data bit.ly/3Y9sQBw

In this article we present a novel “one-pot-two-step” methodology for the synthesis of TCPs that improves the yield and simplifies the isolation and purification of the TCPs bit.ly/3Kf7cZu

hnRNPA1 blocks the kissing-loop contact needed for HCV replication by binding the 5BSL3.2 loop used to pair with 3′X SL2. Our study reveals a new antiviral approach: targeting viral RNA structure bit.ly/49VF33Y

Fission yeast Tpt1 is composed of tandem RNA 2'-phosphotransferase and Yae1 domains, both of which are essential for viability bit.ly/48FujEs

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

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

m⁵C-Rol-LAMP, a simple qPCR-based assay, quantifies m⁵C RNA methylation at single nucleotides and uncovers stress-regulated rRNA modification in bacteria. #LMU_muenchen #lifescimunich #RNA #CRC1309 bit.ly/43AWnr4