RNA Research and Splicing

A positional and combinatorial regulatory code for alternative splicing

This paper introduces SCALE-CLIP, a method to generate comparable RBP binding maps, and defines a positional and combinatorial regulatory code for alternative splicing.

Tumoral Switch in NUMB splicing changes essential transcription pathways and induces malignant properties in tumour cells

The paper identifies a tumour-associated switch in NUMB isoform expression and shows its association with distinct transcriptional clusters and poor survival in breast cancer.

Translation sustains productive Pol II elongation through maintenance of nuclear RNA surveillance

This study shows that ongoing translation sustains productive Pol II elongation and nuclear RNA homeostasis in mouse embryonic stem cells by maintaining RNA surveillance.

Predicting Human mRNA Isoform Levels from Site-Specific Splicing Kinetics in silico

This paper develops a stochastic kinetic model of splicing to predict mRNA isoform levels from site-specific splicing kinetics and validates it under normoxia and hypoxia.

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation

The paper identifies sequence-encoded autoinhibition in fission yeast Dcp2 that regulates mRNA decapping activity and shows how conformational relief is propagated within phase-separated condensates.

RNA-dependent aggregation of a common TEV protease variant alters in vitro biomolecular condensate reconstitution

The paper shows that TEV protease variants can aggregate with RNA, altering in vitro biomolecular condensate formation and highlights the need for validation in RNA-rich systems.

The metastasis susceptibility gene RRP1B is a stress-responsive regulator of nuclear RNA processing and splicing in breast cancer

This paper identifies RRP1B as a stress-responsive regulator of RNA processing and splicing in breast cancer, showing its role in splicing programs and tumor aggressiveness.

Molecular basis of polyadenylated RNA fate determination in the nucleus

The paper identifies a nuclear mechanism that determines the fate of polyadenylated RNAs by distinguishing between functional and non-functional transcripts through the opposing actions of PAXT and TREX-2.

Molecular determinants of Hrp1-RNA recognition underlying yeast RNA Polymerase II transcription attenuation

The paper identifies Hrp1's role in RNA Polymerase II transcription attenuation in yeast by showing its binding to attenuator RNAs and the impact of mutations on this interaction.

A minimal thermodynamic theory for re-entrant liquid-liquid phase separation regulated by small molecules

The paper develops a thermodynamic model to explain re-entrant liquid-liquid phase separation regulated by small molecules, showing how concentration-dependent interactions drive nonmonotonic condensate formation.

Domain-specific regulation of PABPN1 uncouples aggregation from function and enables therapeutic rescue

This study identifies a stabilized PABPN1 variant, trPAB, that reduces aggregation and restores function in OPMD and bladder cancer models, supporting its potential as a gene therapy.

Extended poly(A) tails are a shared feature of herpesvirus mRNAs

The paper uses nanopore sequencing to show herpesvirus mRNAs have longer poly(A) tails than cellular or other viral transcripts, suggesting a unique mechanism for enhancing gene expression.

Reaction-diffusion condensation generates a regulatable landscape for self-organizing subcellular structures

The paper introduces RIPPLE, a synthetic system that uses reaction-diffusion waves to generate tunable subcellular structures by coupling IDR sequences to a two-protein RD circuit.

Dual Effect of RNA-like Polyelectrolytes on Stability and Dynamics of Biomolecular Condensates: A Tale of Competitive Short and Long-range Interactions

This study investigates how RNA-like polyelectrolytes affect the stability and dynamics of biomolecular condensates by altering short and long-range interactions.

Trailer Hitch tunes condensate phase behavior and mRNA partitioning to regulate P-body homeostasis during Drosophila melanogaster oogenesis

This study shows that Trailer Hitch regulates P-body structure and mRNA partitioning in Drosophila oogenesis by modulating condensate dynamics and mRNA stability.

Systematic Profiling and Functional Characterization of Alternative Splicing in C. elegans Olfactory Learning

The paper profiles alternative splicing changes in C. elegans during learning and shows AS regulates learning through a distinct mechanism from transcript abundance changes.

Improving splice site usage prediction with SPLAIRE

The paper evaluates splicing models, identifies performance gaps, and introduces a cell-type-specific model for improved splice site prediction in human airway epithelial cells.

SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction

SpliceSelectNet predicts splice sites from DNA sequences using a hierarchical Transformer model, achieving state-of-the-art performance and capturing long-range regulatory effects.

Robust mammalian RNA localization elements are complex and multipartite

The paper identifies that mammalian RNA localization elements are large, complex, and multipartite, requiring specific subsequences for function.

Dissecting Rate-Limiting Processes in Biomolecular Condensate Exchange Dynamics

This paper develops a reaction-diffusion model to analyze biomolecular condensate exchange dynamics, identifying multiple rate-limiting processes and a pore-mediated pathway that decouples exchange timescale from condensate size.

Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS

This paper uses long-read cDNA sequencing to identify novel transcripts and spliceosome-mutant-enriched isoforms in AML and MDS, providing a resource for improving short-read RNA-seq analyses.

A Spatially Resolved Atlas of Alternative Polyadenylation Across 18 Human Tissues and 76 Disease States

The paper constructs a spatially resolved APA atlas across 18 human tissues and 76 diseases using SpatialAPA, revealing organ-specific APA patterns and their role in disease progression.

The molecular determinants of PABPC-mediated deadenylation rate

This study investigates how PABPC1 binding and 3' UTR sequences influence deadenylation rates, revealing two mechanisms by which UTR sequences modulate deadenylation kinetics.

mRNA 3'UTRs chaperone intrinsically disordered regions to control protein activity

The paper shows that mRNA 3'UTRs act as chaperones for intrinsically disordered regions (IDRs) to regulate protein activity by promoting IDR-IDR interactions and preventing domain folding interference.

U1 snRNP and RNA polymerase II interaction is predominantly mediated by Prp40 rather than U1-70K in yeast

The paper investigates the interaction between U1 snRNP and RNA polymerase II in yeast, finding that Prp40, not U1-70K, mediates this interaction, contrasting with the human system.

A U1-U3 snRNA-snoRNA interaction couples SF3B1 mutation to chromatin-state rewiring and genome instability

This paper identifies a U1-U3 snRNA-snoRNA interaction that links SF3B1 mutations to chromatin-state changes and genome instability, with therapeutic potential through antisense oligonucleotides.

Dissection of Poly(A)-binding protein (PABPC) cellular function using degron-mediated depletion with replacement

This paper develops a protein-replacement platform to study PABPC function by degrading endogenous PABPC1/4 and expressing engineered variants, revealing domain-specific roles and functional divergence.

Mapping high resolution, multidimensional phase diagrams of physiological protein condensates

This study introduces ExVivo PhaseScan to generate high-resolution phase diagrams of physiological protein condensates and reveals how FUS mutations cause liquid-to-solid transitions in stress granules and nucleoli.

In vivo binding by Arabidopsis SPLICING FACTOR 1 shifts 3' splice site choice, regulating circadian rhythms and immunity in plants

This study identifies AtSF1's role in regulating 3' splice site choice in Arabidopsis, linking splicing to circadian rhythms and immunity.

The E. coli DEAD box ATPase CsdA, is a NAD+ capped RNA binding protein

This study identifies CsdA as the first NAD+ cap reader protein in E. coli, showing it binds NAD+ capped RNA and enhances decapping activity.