RNA Research and Splicing

Oxygen partitioning into biomolecular condensates is governed by protein density

The paper investigates oxygen partitioning into biomolecular condensates and finds that oxygen concentration varies with protein density and chain length.

Decoding the RNA Splicing Network in HNRNPH2-R114W Brain Organoids

This study investigates the impact of the HNRNPH2-R114W mutation on RNA splicing in human brain organoids, identifying junction-level dysregulation and potential therapeutic targets.

Natural language-based representation and modeling of RBP binding

The paper introduces a natural language-based approach to model RBP binding by decomposing RNA sequences into linguistic regions and using iterative relabeling for prediction.

The kinetics of ribonucleoprotein granules

The paper develops an in vitro single-molecule assay to measure RNP granule assembly and disassembly kinetics, revealing pathway-dependent behavior and non-equilibrium dynamics.

MAPK signaling modulates the partition of DCP1 between P-bodies and stress granules in plant cells

The paper investigates how MAPK signaling affects DCP1 localization between P-bodies and stress granules in plant cells, showing phosphorylation shifts DCP1 from P-bodies to stress granules.

ASPECT: Alternative Splicing Event Classification with Transformers

ASPECT classifies alternative splicing events using a transformer-based model, achieving strong performance on multiple tasks and showing applicability to cancer-related splicing events.

Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization

The paper introduces RLP, a method to map subcellular RNA localization in single cells, revealing widespread heterogeneity undetectable by bulk methods.

Amplified MS2 labeling reveals heterogeneous dynamics of RNA granules in the live murine brain

This paper introduces a method to visualize RNA granules in live mouse brain tissue, revealing heterogeneity in mRNA dynamics across neurons and glial cells.

On the Use of Double Mutant Cycles to Probe the Molecular Interactions in Biomolecular Condensates

This study uses double mutant cycles to analyze molecular interactions in biomolecular condensates, finding additive and non-additive contributions to phase separation propensity.

mRNA Imprinting: transcription apparatus can remotely control cytoplasmic post-transcriptional mechanisms by dozens of proteins

The paper identifies proteins involved in mRNA imprinting using a novel high-throughput method, showing that transcription machinery can regulate cytoplasmic processes like translation and mRNA decay.

eRNAs Modulate mRNA Stability and Translation Efficiency to Bridge Transcriptional and Post-transcriptional Gene Regulation

The paper characterizes eRNA decay kinetics and identifies their role in modulating mRNA stability and translation efficiency across human cell types.

Synthetic germ granules reveal a direct role of Vasa/DDX4 in RNA localization and translational activation

This study uses synthetic biology to reconstitute germ granules and identifies Vasa/DDX4 as essential for RNA localization and translational activation.

Correction of multiple splicing mutations associated with CFTR exon 18 using a single exon-specific U1 snRNA

This study develops a platform to screen and rescue multiple splicing mutations using a single exon-specific U1 snRNA, showing effectiveness in rescuing 3 and 5 splice site mutations in CFTR exon 18.

Slow diffusion limits phosphorylation in a biomolecular condensate

The paper shows that slow diffusion in biomolecular condensates limits phosphorylation kinetics, with phosphorylation rates strongly correlated to substrate diffusion coefficients.

Nuclear Speckles are Regulatory Hubs for Viral and Host mRNA Expression During HSV-1 Infection

This paper shows that nuclear speckles regulate viral and host mRNA processing and export during HSV-1 infection, with viral transcripts uniquely relying on speckles for export.

The TUTase URT1 regulates the transcriptome of seeds and their primary dormancy

This study identifies URT1 as the main enzyme for mRNA uridylation in Arabidopsis, showing its role in shaping the seed transcriptome and regulating primary dormancy.

Alternative polyadenylation mediated by CPSF5 regulates pro-inflammatory gene expression

The paper shows that CPSF5 repression leads to transcript shortening and increased pro-inflammatory gene expression in macrophages and sepsis patients.

RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions

RBPscan profiles RBP-RNA interactions in vivo by integrating RNA editing with MPRA, quantifying binding strength and identifying motifs across species.

RNAMaRs: an interpretable framework for inferring multivalent RNA Motifs and cognate Regulators of Splicing

RNAMaRs infers RNA motifs and their regulatory proteins by integrating motif discovery, binding data, and splicing responses, showing consistent prioritization of perturbed regulators in ENCODE datasets.

Decoding the MYC locus reveals a druggable ultraconserved RNA element

The paper maps the functional fitness landscape of the MYC locus, identifies an ultraconserved RNA element critical for MYC function, and shows it can be targeted to kill MYC-addicted cancer cells.

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain

The paper introduces spatial NT-seq to map RNA turnover and stability in the mouse brain, revealing spatial heterogeneity and kinetics scaling mechanisms in response to ECS.

A stress-dependent postembryonic role for the core CPA factor CFIM-1 in germline integrity

This study identifies a stress-dependent role for the CPA factor CFIM-1 in maintaining germline integrity in C. elegans by regulating transcript isoform abundance.

Global mRNA 3'UTR lengthening in small-cell neuroendocrine carcinoma

The paper identifies global 3'UTR lengthening in SCNC through APA and develops a neural network model to classify SCNC using APA signatures.

Alphaviral capsid proteins inhibit stress granule assembly via competitive RNA binding with G3BP1

This study identifies how alphavirus capsid proteins inhibit stress granule assembly by competing with G3BP1 for RNA binding, revealing a conserved mechanism across alphaviruses.

The spliceosome assembles on excised linear introns to protect them from degradation

The paper shows that spliceosomes protect linear introns from degradation by assembling on them, and this process is conserved across stress and unstress conditions.

The sequence context of RG/RGG motifs determines condensate formation, transportin-1 binding and chaperoning

The paper investigates how sequence context of RG/RGG motifs influences condensate formation, transportin-1 binding, and chaperoning using bioinformatics and experimental analysis.

Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease

The paper introduces TM-map, a method to map RNA-binding protein binding sites on RNA with high resolution, validated on bacteriophage MS2 coat protein and Drosophila FMRP.

A structured RNA balances DEAD-box RNA helicase function in plant alternative splicing control

The paper identifies a structured RNA element in DEAD-box RNA helicase genes that regulates alternative splicing through a negative feedback loop in Arabidopsis thaliana.

Manipulation of alternative splicing of IKZF1 elicits distinct gene regulatory responses in T cells

The paper investigates how alternative splicing of IKZF1 affects gene regulation in T cells, finding significant changes in gene expression and chromatin accessibility.

Sequence-based models for RNA-Protein interactions imputation might be insufficient for novel signal prediction in eCLIP data

The paper presents a machine learning framework to predict RNA-protein interactions using eCLIP data and shows its limitations in extrapolating to proteins without such data.