RNA

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

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

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

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

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

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

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

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. bit.ly/43AWnr4 #LMU_muenchen #lifescimunich #RNA #CRC1309

Conserved protein Seb1 that interacts with RNA polymerase II and RNA is an anti-pausing transcription elongation factor bit.ly/4pbUQzQ

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

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

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

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