RNA Research and Splicing

Oncogenic NOVA1 expression dysregulates alternative splicing in breast cancer

This study shows that NOVA1 overexpression in breast cancer disrupts alternative splicing, particularly in genes related to cell communication and cytoskeleton, and is linked to worse outcomes in Luminal A tumors.

Sex and Alternative Splicing in Disease: a meta-analytic approach to identify interactions

The paper uses a meta-analytic approach to identify sex-dependent splicing interactions in type 1 diabetes, finding higher prevalence in CD4 T cells than CD8 T cells.

A self-consistent model for phase separation and active processes in biomolecular condensates

The paper develops a self-consistent model to study phase separation and active processes in biomolecular condensates, showing how scaffold activity regulates phase behavior and enhances client transport near stability thresholds.

Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation

The paper investigates IDR-IDR interactions in synthetic systems to assess their ability to mediate specific condensate formation, finding high promiscuity among some IDRs and specific recognition in others.

A molecular grammar for programmable multiphase protein-RNA vesicles

This study identifies molecular rules governing the formation of multiphase protein-RNA condensates and demonstrates how sequence and composition can program their architecture.

The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in early Caenorhabditis elegans embryos

The paper identifies SPN-4 as a specificity factor for CCR4-NOT-dependent clearance of maternal mRNAs in C. elegans embryos, showing its role in targeting specific transcripts for decay.

Allele-specific splicing modulates protein isoforms and Alzheimer's risk

The paper identifies allele-specific splicing events in brain tissues linked to Alzheimer's disease risk and functional genetic variation.

Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins

This study identifies ZC3H7A and ZC3H7B as RNA-binding proteins that regulate mRNA stability and translation by targeting non-optimal A/U3 codons.

TgmRHel drives unified RNA processing of coxI mRNA generated from a complex mitochondrial genomic context

The paper shows that TgmRHel processes coxI mRNA precursors generated from a recombining mitochondrial genome into a mature transcript, essential for parasite survival.

PAIR-link: a ligation-free strategy that joins two RNAs into a single sequence-preserving chimeric cDNA

PAIR-link joins two RNAs into a single chimeric cDNA without crosslinking, fragmentation, or ligation, preserving full sequence information.

Generative modeling for RNA splicing predictions and design

This paper introduces TrASPr+BOS, a generative AI model for predicting and designing RNA to achieve tissue-specific splicing outcomes, showing improved performance over existing methods.

Many-body Interaction Competition Drives Reentrant Phase Transitions

This paper shows how introducing reversible dimerization into a Flory-Huggins model creates an effective three-body repulsion, explaining reentrant phase transitions in biomolecular condensates.

Microexon alternative splicing and feeding behavior in C. elegans.

This study shows that microexon alternative splicing in C. elegans changes with developmental stage and is influenced by food availability and DNA topology, affecting feeding behavior.

Augmenting Transcriptome Annotations through the Lens of Splicing Evolution

TENNIS predicts unannotated isoforms and refines existing annotations using an evolution-based model of alternative splicing, validated by deep long-read RNA-seq.

More than 100 dual coding regions have evidence for selection constraints in both reading frames

The paper identifies 105 dual coding regions under purifying selection in both reading frames, with many linked to brain development and neural functions.

RNA-binding proteins activate transcription through defined molecular grammars

The paper identifies RNA-binding proteins (RBPs) that activate transcription through molecular grammars similar to transcription factors, revealing their role in transcriptional regulation and RNA processing.

Multi-omic screening identifies RBMXL3 as a primate-specific RNA-binding protein and candidate regulator of RNA metabolism in human spermatogenesis

This study identifies RBMXL3 as a primate-specific RNA-binding protein that regulates RNA metabolism and suppresses LINE-1 retrotransposition in human spermatogenesis.

Active RNA synthesis patterns nuclear condensates

The paper investigates how active RNA synthesis influences nuclear condensate patterning by studying nucleolar fibrillar centers and shows that RNA synthesis affects their size, number, and spacing.

NF1 splicing reprograms ERα signaling to promote luminal breast cancer progression

This paper identifies an alternatively spliced NF1 isoform, NLS SE, that promotes luminal breast cancer progression by disrupting nuclear neurofibromin function and reprogramming ER signaling toward post-transcriptional regulation.

Pontocerebellar Hypoplasia linked mutations of the deadenylase Target of EGR1 (TOE1) impair thermal stability, ribonuclease activity, and oligomerization.

This study investigates how PCH7-linked TOE1 mutations affect thermal stability, ribonuclease activity, and oligomerization, revealing their impact on TOE1 biochemistry.

A BRRF1-CCR4-NOT axis underlies conserved transcriptome-wide loss of splicing fidelity during gammaherpesvirus reactivation

The paper identifies BRRF1 as a key driver of transcriptome-wide splicing defects during gammaherpesvirus reactivation by hijacking the CCR4-NOT complex.

OpenSplice: the impact of half a million mutations on the alternative splicing of 600 human exons

OpenSplice quantifies the impact of over 590,000 variants on the splicing of 600 human exons, providing insights into splicing regulatory mechanisms and enabling machine learning model evaluation.

Biomolecular condensation of cMLCK enables myosin motor phosphorylation in the heart

This study shows that cMLCK forms biomolecular condensates that enhance myosin motor phosphorylation in cardiac muscle cells, revealing a mechanism for regulating heart contractile function.

New insight into the RNA-chaperon activity of nucleobindin 1

The paper identifies three RNA-binding regions in NUCB1 and demonstrates its ability to interact with two RNA fragments, suggesting a role in RNA-chaperone activity.

SpliceRead: Improving Canonical and Non-Canonical Splice Site Prediction with Residual Blocks and Synthetic Data Augmentation

SpliceRead improves canonical and non-canonical splice site prediction using residual blocks and synthetic data augmentation, outperforming existing models across multiple metrics.

Divergent RNA structures support accurate splicing of the SF3B1-sensitive MAP3K7 intron

The paper investigates how RNA sequence and structure influence splicing of the MAP3K7 intron, showing that branchpoint mutations strongly affect cryptic splice-site usage and that structural changes in RNA binding protein hotspots correlate with splicing outcomes.

Dramatically reduced spliceosome, intronome, and splicing efficiency in Cyanidiococcus yangmingshanensis and Cyanidium caldarium

The paper analyzes the spliceosome, intronome, and splicing efficiency in three extremophilic red algae, finding reduced spliceosome components, low splicing efficiency, and conserved splice site sequences.

Splicing of ultraconserved poison exons controls mitotic fidelity and stem cell viability

This study shows that ultraconserved poison exons regulate mitotic splicing fidelity and stem cell viability by controlling SR protein levels and splicing networks.

Isotope-Free Mapping of protein:RNA Interactions Using fCRAC and trxtools

The paper introduces fCRAC, a method for high-resolution mapping of protein:RNA interactions without radioactive labeling, and provides trxtools for analysis, revealing interactions of CYCLON/CCDC86 with rRNA, tRNA, and ncRNAs.

Muscleblind-like proteins dimerize by forming disulfide bonds to regulate alternative splicing and pathogenic RNA foci formation

This study identifies disulfide bonds mediating MBNL1 and MBNL2 dimerization, showing their role in alternative splicing regulation and RNA foci formation in myotonic dystrophy.