RNA Research and Splicing

New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

This study characterizes the subcellular localization and nuclear import mechanisms of yeast RNA exosome subunits, revealing their nucleolar distribution and interactions with importins and cofactors.

PI3K/AKT Signaling Mediates Stress-Inducible Amyloid Aggregation Through c-myc

The paper identifies PI3K/AKT signaling as a mediator of stress-induced amyloid aggregation through c-myc activation and repression of GSK3 degradation.

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

This study identifies SFSWAP as a negative regulator of OGT intron detention and global pre-mRNA splicing, showing its role in decoy exon inclusion and intron retention.

c-MYC can Form Phase Condensates via its DNA Binding Domain

This study shows c-MYC can form phase condensates using its DNA binding domain, using optoDroplet system for dynamics analysis.

The spliceosome component U1-70k loads nascent transcripts onto FVE/SGS3 via co-condensation to embark on RNA silencing

The paper identifies U1-70k as a novel spliceosome factor that facilitates RNA silencing by co-condensing with SGS3 to load nascent transcripts into the PTGS pathway.

ZBP1 Senses Splicing Aberration through Z-RNA to promote Cell Death

This study shows that spliceosome inhibition generates Z-RNA, sensed by ZBP1 to trigger necroptosis in response to splicing aberrations.

Genome-wide mapping of mesoscale neuronal RNA organization and condensation

The paper introduces RNA-SPRITE to map RNA-RNA spatial proximity genome-wide, revealing conserved mRNA organization and colocalization driven by shared motifs and functional relationships.

Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2

This study identifies UPF2's RNA-binding and unfolding activities, showing its role in stabilizing single-stranded RNA and supporting NMD factor interactions.

Compartmentalization of mRNA and Translation by Desmosomes

The paper identifies desmosomal proteins as essential for cortical compartmentalization of translation and mRNA, revealing dynamic regulation of the cortical translatome in response to wounding.

Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation

The paper compares disease-linked missense mutations in the RNA exosome using yeast models to identify shared and distinct functional consequences in translation.

Splice-switching ASOs targeting an Alu-derived exon in the AURKA 5'UTR collapse an SRSF1-AURKA-MYC oncogenic circuit in pancreatic cancer

This study identifies an SRSF1-AURKA-MYC oncogenic circuit in pancreatic cancer and shows that splice-switching ASOs targeting AURKA 5'UTR splicing disrupts this circuit, reducing cell viability and inducing apoptosis.

Interactions between the picornavirus 3C(D) main protease and RNA induce liquid-liquid phase separation

This study shows that the picornavirus 3C protease binds RNA and induces liquid-liquid phase separation, which may have implications for viral replication and stress granule dynamics.

Controlled and orthogonal partitioning of large particles into biomolecular condensates

This study demonstrates that large particles can be controlled and orthogonally partitioned into biomolecular condensates through strong particle-condensate interactions, using polymer nanoparticles with tailored surface chemistries.

Differential interactions determine anisotropies at interfaces of RNA-based biomolecular condensates

The paper investigates anisotropies in RNA-based biomolecular condensate interfaces, finding that purine-rich RNAs drive phase separation while pyrimidine-rich RNAs accumulate at interfaces, with distinct motion patterns observed using single-molecule imaging.

RNA Modifications and Prp24 Coordinate Lsm2-8 Binding Dynamics during S. cerevisiae U6 snRNP Assembly

This study uses CoSMoS to analyze how RNA modifications and Prp24 influence Lsm2-8 binding dynamics during U6 snRNP assembly in yeast.

Roquin exhibits opposing effects on RNA stem-loop stability through its two ROQ domain binding sites

This paper investigates how Roquin's two ROQ domains interact with different regions of the Ox40 mRNA 3UTR, revealing opposing effects on RNA structure stability and mRNA decay.

Genetic and functional analysis of unproductive splicing using LeafCutter2

LeafCutter2 identifies and quantifies unproductive splicing events from RNA-seq data, revealing their role in gene regulation and disease, including Alzheimer's.

OmniSplice: detection of non-canonical splicing events from RNA-seq

OmniSplice detects non-canonical splicing events from RNA-seq by analyzing reads overlapping annotated exon ends without assuming predefined splice-junction structures, revealing widespread splicing defects in Drosophila and mouse mutants.

Perturbing RNA localization for functional study in neurons

This study introduces CRISPR-TO to manipulate RNA localization in neurons, showing it affects neurite outgrowth and axonal regeneration.

Decoding RAP1's Role in Yeast mRNA Splicing

This study identifies RAP1's role in alternative splicing, particularly intron retention, and links it to nonsense-mediated decay in yeast.

RNA Editors Sculpt the Transcriptome During Terminal Erythropoiesis

The paper identifies ZCCHC6 and DIS3L2 as key regulators of RNA decay during terminal erythropoiesis, showing their role in post-transcriptional globin switching and {gamma}-globin stabilization.

A TranSNP in the DDIT4 mRNA can impact its translation efficiency and modulate p53-dependent responses in cancer cells

The paper identifies a tranSNP in DDIT4 mRNA that affects translation efficiency and modulates p53-dependent responses in cancer cells.

A unique mechanism of snRNP core assembly

The paper identifies two distinct pathways for snRNP core assembly in budding yeast, revealing a unique mechanism that explains the non-essentiality of assembly chaperones.

Pooled scanning of protein variants identifies novel RNA-binding mutants

The paper introduces RBR-scan, a method to identify RNA-binding mutants by measuring affinity of protein variants, and validates it with known and novel mutants in SRSF2.

A nuclear RNA degradation code for eukaryotic transcriptome surveillance

The paper identifies a nuclear RNA degradation code (NRDC) that recognizes transcripts with both a 5' splice site and a poly(A) junction, leading to their degradation and contributing to disease.

Disrupting Splicing Regulation to Rescue β-Catenin: A Novel Approach for Treating CTNNB1-Haploinsufficiency Disorder

This study uses spliceosome-mediated RNA trans-splicing to restore β-catenin production in CTNNB1 syndrome, showing improved trans-splicing efficiency with optimized PTMs.

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

Biosurfer identifies sources of protein isoform diversity by analyzing long-read RNA-seq data, revealing common mechanisms like alternative transcription start sites and 'ragged codons'.

Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing

This study uses direct RNA nanopore sequencing to analyze allele-specific pre-mRNA maturation in human lymphoblastoid cell lines, revealing splicing order differences and SNP-splicing associations.

Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles

This study identifies Arc/Arg3.1 as a regulator of PABPN1 nuclear speckles through direct binding, impacting mRNA processing during neuronal activity.

Beyond the Gene in Genetics: How Isoform-Resolved Analysis Empowers the Study of Both Common and Rare Genetic Variation

This study shows that analyzing genetic variants at the isoform level reveals significant associations with human phenotypes and rare variants, highlighting the importance of isoform-resolved analysis in genetics.