RNA Research and Splicing

The paper identifies widespread polycistronic-like transcripts in Populus species using Nanopore DRS, revealing their molecular features and regulatory patterns.

The paper tracks splicing intermediates in human cells using ultra-deep sequencing and finds pervasive usage of low-fidelity splice sites associated with genomic features that promote splicing noise.

This study shows SRSF5 is critical for paraspeckle assembly and dynamics, with stress-induced changes and compensatory effects on TDP-43 and NEAT1.

The paper investigates the functional roles of multiple Tudor domains in Drosophila germline formation and finds that they are non-redundant and essential for germ cell development.

The paper updates the wRBP1.0 compendium of C. elegans RNA-binding proteins to 928 proteins, cataloging their expression and developmental phenotypes.

This paper uses label-free fluorescence microscopy to study biomolecular condensates, revealing their multiphase organization and dynamic properties without exogenous labels.

The paper investigates how lysine acetylation of RNA binding proteins affects alternative pre-mRNA splicing using PTBP1 as a model.

This study identifies KI-DX-014, a small molecule that binds DDX21 and modulates its RNA-related functions, revealing a new therapeutic approach for targeting DEAD-box proteins.

This study shows SUMO2 stabilizes HLB interactions and facilitates U7 snRNP assembly, preventing histone mRNA polyadenylation.

The paper shows that TDP-43 loss causes cryptic splicing events that are masked by nonsense-mediated decay, and inhibiting this decay reveals hundreds of novel splicing events.

This study shows that RNase L, an antiviral nuclease, represses transcription by reducing RNA polymerase II elongation, particularly affecting immune-related genes.

AVJ16 inhibits IGF2BP1 in lung adenocarcinoma cells and xenografts, reducing proliferation, enhancing apoptosis, and preventing tumor growth.

The paper investigates how cell size affects P-body assembly in yeast, finding a nucleation distance of 2.2 micrometers that links cell geometry to condensate formation.

This study identifies TRIM28's role in pre-mRNA splicing through phosphorylation and SUMOylation interactions with USP39, showing its impact on alternative splicing patterns.

This study shows ISRIB enhances TIA-1 phase separation and promotes its aggregation in vitro, with RNA mitigating this effect.

This paper shows that PKA-dependent phosphorylation drives stress granule maturation during prolonged starvation, delaying disassembly and promoting cell survival.

The paper benchmarks differential transcript usage analysis tools across static and dynamic conditions, finding optimal tools for different data types and experimental settings.

This study characterizes Arabidopsis RS2Z32 and RS2Z33 splicing factors, showing their nuclear localization, RNA binding specificity, and interactions with other SR proteins.

This study presents the cryo-EM structure of the snRNA export complex and shows how PHAX synergistically binds components to facilitate snRNA export.

This study predicts globular protein partitioning into condensates using hydration free energy, showing strong correlation with partition coefficients and highlighting limitations of the approach.

The paper shows that IL-6 induces altered polyadenylation in SERPINA1, increasing long 3UTR isoforms that repress A1AT protein expression during inflammation.

This paper shows that SMAUG1 forms condensates via its disordered region and that 14-3-3 proteins dissolve these condensates through phospho-regulated interactions.

The paper develops an inducible tethered function assay (iTFA) to analyze the regulatory effects of RNA-binding protein domains, specifically demonstrating its application to YBX3.

This study shows that repeat RNAs form nanoscale clusters within biomolecular condensates, driven by sequence features and RNA secondary structure, and that G3BP1 buffers these interactions.

This paper identifies Rim4 as a meiotic thermal sensor that forms reversible condensates triggered by heat, promoting stress granule assembly and protecting meiotic processes from thermal stress.

This study identifies the RNA-binding preferences of human FASTK, showing it binds single-stranded G-rich RNA and G-quadruplexes, and protects mitochondrial mRNAs from degradation.

This paper introduces PTM-POSE, a computational pipeline to analyze how alternative splicing affects post-translational modifications, and finds that 32% of PTMs are excluded from at least one Ensembl isoform.

The paper reports the cryo-EM structure of a transcribing Pol II-U1 snRNP complex with DSIF and SPT6, showing how phosphorylated Pol II and SPT6 interact with U1 snRNP to facilitate spliceosome assembly and transcription processivity.

This study uses long-read RNA sequencing to analyze transcript diversity and regulation in human fibroblasts, induced pluripotent stem cells, and cortical neurons, revealing transcript-specific changes in disease-related genes.

This study identifies age-related changes in transcript variants in mouse ovaries, revealing that differential expression of alternative transcripts is often overlooked by traditional gene expression analyses.