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
