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

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

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

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

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

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

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

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

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

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

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

T-box-i is a novel, effective inhibitor of T-box riboswitches with antimicrobial activity against Staphylococcus aureus bit.ly/4nyMmSE

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

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

Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery bit.ly/4n38pB3

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