RNA Research and Splicing

Impact of U2-type introns on splice site prediction in Arabidopsis thaliana using deep learning

This study uses deep learning to show that shorter and multiple U2-type introns improve splice site prediction in Arabidopsis thaliana.

Interpretable Distillation Reveals that Deep-learning-based Splicing Models Suffer from Pervasive Confounders and Blind Spots

This study reveals that deep-learning-based RNA splicing models have confounders and blind spots, leading to poor performance on non-reference sequences.

Protocol for capturing the RNA-binding proteome from plants using orthogonal organic phase separation

The paper describes a protocol for isolating RNA-binding proteins from plants using UV-crosslinking and organic phase separation, followed by proteomics analysis.

The pos-1 3' untranslated region governs germline specification and proliferation to ensure reproductive robustness

The paper shows that the pos-1 3'UTR regulates POS-1 expression in C. elegans, affecting germline specification and reproductive robustness under stress.

Dynamic changes in mRNA isoform usage during human retinal organoid development

The paper uses long-read RNA sequencing to study dynamic mRNA isoform changes during human retinal organoid development, revealing splicing patterns and allelic imbalance.

Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth

The paper shows that CLB2 mRNA localization to the bud via the She2/She3 complex enhances translation, linking cell growth to cell cycle progression through a ZIP-code element in the coding sequence.

Regulation of alternative polyadenylation events by PABPC1 affects erythroid progenitor cell expansion

This study identifies PABPC1 as a key regulator of alternative polyadenylation in erythroid progenitor cells, showing its role in cell expansion and differentiation through APA shifts.

Long-read transcriptomics of purified human cortical cell types exposes glial isoform complexity and disease-relevant transcript architecture

The paper uses long-read transcriptomics to analyze human cortical cell types, revealing extensive isoform diversity in glial cells and identifying novel transcripts with disease-relevant splice variants.

Clinical Implications of SRPK1 Expression in Human Tumours: A Comprehensive Pan-Cancer Analysis Based on Multi-Omics Databases

This study investigates SRPK1 expression across multiple cancer types using multi-omics data, finding its association with poor survival and chemoresistance.

Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations

The paper investigates snaR-A, a cancer-associated ncRNA, showing it interacts with splicing factors and disrupts mRNA processing, contributing to cancer progression.

Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq

CRISPore-seq combines CRISPR perturbations with long-read transcriptomics to detect alternative splicing changes, revealing that exon skipping is common and linked to RNA-binding protein perturbations.

Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in post-transcriptional repression of starvation-induced pathways

The paper shows Scd6 and Edc3 redundantly work with Dhh1 to repress mRNA decay of starvation-induced pathways in yeast.

Timing of transcription controls the selective translation of newly synthesized mRNAs during acute environmental stress

The paper shows that during acute glucose withdrawal in yeast, newly synthesized stress mRNAs escape translational repression while pre-existing mRNAs are repressed, revealing a timing-based coordination of transcriptional and translational responses.

Expression and Purification of Full-Length hnRNPA2B1 for Biophysical Characterization of Liquid-Liquid Phase Separation

This study reports the successful expression and purification of full-length hnRNPA2B1, enabling its use in studying liquid-liquid phase separation and aggregation.

The Implications of Alternative Splicing Regulation for Maximum Lifespan

This study identifies conserved alternative splicing events associated with maximum lifespan across mammals, showing distinct patterns in the brain compared to peripheral tissues.

RAPMS 2.0 Improves Specificity and Throughput for Proteomic Identification of RNA Binding Proteins

RAP-MS 2.0 improves specificity and throughput for identifying RNA-binding proteins by reducing background and enabling reuse of lysate for multiple RNA captures.

Mammalian Pabpc4 is non-essential for development, but has roles in growth, post-natal survival and haematopoiesis

This paper shows that Pabpc4 is not essential for development but is important for post-natal growth, survival, and hematopoiesis in mice, with effects on red blood cell morphology.

PTBP1 Depletion in Mature Astrocytes Reveals Distinct Splicing Alterations Without Neuronal Features

This study shows that PTBP1 depletion in astrocytes causes unique splicing changes without neuronal features, suggesting PTBP1 alone is insufficient for neuronal reprogramming.

Multiplexed smFISH reveals the spatial organization of neuropil localized mRNAs is linked to abundance

The paper uses multiplexed smFISH to analyze the spatial organization of 15 synaptic neuropil localized mRNAs in rodent hippocampus, finding that colocalization patterns scale with mRNA abundance.

Multiple Quality Control Checkpoints Safeguard Small Nuclear RNA Biogenesis and Prevent Assembly of Aberrant Spliceosomes

The paper identifies quality control checkpoints in snRNA biogenesis that prevent defective snRNAs from forming aberrant spliceosomes and causing pre-mRNA splicing defects.

Tag with Caution - How protein tagging influences the formation of condensates

This study examines how protein tags affect condensate formation in different contexts and identifies charge as a key factor influencing condensation behavior.

Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements

The paper shows Ku prevents aberrant mRNA splicing caused by intronic antisense Alu elements, which affects RNA metabolism and cell viability.

RNA switch model for localization and translation of the myelin basic protein mRNA

The paper identifies a structured RNA region, MLS, necessary and sufficient for Mbp mRNA transport to oligodendrocyte projections and shows it interacts with hnRNP-F, suggesting a structural switch model for mRNA transport to translation.

Distinct cis-acting elements combinatorically mediate co-localization of mRNAs encoding for co-translational interactors in cytoplasmic clusters in S. cerevisiae

Integrative profiling of condensation-prone RNAs during early development

The paper identifies a class of condensation-prone RNAs during early development and reveals their sequence and structural features using deep learning.

Phenotypic impact of individual conserved neuronal microexons and their master regulators in zebrafish

The paper investigates the phenotypic impact of individual conserved neuronal microexons and their regulators in zebrafish, finding that microexon deletions have mild effects while Srrm3/4 loss causes severe neurodevelopmental and behavioral changes.

Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function

This study removes 45 microexons in zebrafish using CRISPR/Cas9 and finds minimal developmental impact on brain morphology and function, with some exceptions in specific microexons.

FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

This paper shows that FRG1 regulates nonsense-mediated mRNA decay by modulating UPF1 levels through its interaction with the spliceosome and exon junction complex.

Astrocytic Nonsense-mediated mRNA decay regulates calcium signaling to support synapse function and influence anxiety-like behavior

This study shows that NMD in astrocytes regulates calcium signaling and synapse function, affecting anxiety-like behavior in mice.

Differential contribution of the RNA recognition motifs to SRSF1 protein interaction network

This study identifies the differential roles of SRSF1's RNA recognition motifs in protein interactions using SILAC proteomics.