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

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

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

LC-MS based quantification of m6A, m6Am and inosine challenges the view of m6A as a dynamic modification and shows m6Am potential as a dynamic, reversible RNA methylation mark in total poly(A) RNA bit.ly/4hnU4vI

Ordered Two-Template Relay (OTTR) appends adapters to RNA end-to-end cDNA during reverse transcription. We optimized end-precision and low-input, gel-based or automation-compatible protocols bit.ly/4gRL6al

The methylation status of protein DRBD18 influences its role in the U-indel RNA editing of A6 and COIII mRNAs bit.ly/4jrnQ4P

Welcome to rRFtargetDB! It is a database of rRNA-derived fragments, a novel class of emerging post-transcriptional regulators of gene expression likely binding to transcripts of their target genes bit.ly/40kAqtH

Intra-host quasispecies as disease determinant, and precursor of a diversifying virosphere bit.ly/3Cbc0uN

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 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