RNA Research and Splicing

HP-Bodies - Ancestral Condensates that Regulate RNA Turnover and Protein Translation in Bacteria

The paper identifies polyphosphate as a scaffold for phase-separated condensates in bacteria and humans, showing its role in RNA turnover and translation.

mRNA stability fine tunes gene expression in the developing cortex to control neurogenesis

The paper shows that RNA stability controls neurogenesis in the developing cortex by regulating gene expression through the CCR4-NOT complex.

Nucleotide-specific RNA conformations and dynamics within ribonucleoprotein condensates

This study uses X-ray scattering and simulations to analyze RNA conformational changes in RNP condensates, revealing sequence-specific dynamics and interactions with polybasic peptides.

Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts

The paper shows that stress granules sequester the CCR4-NOT complex, leading to poly(A) tail lengthening and increased survival transcript abundance under stress.

Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms

Shiba and scShiba systematically identify differential RNA splicing across RNA-seq platforms with high accuracy and low false positives, even with small sample sizes.

Integrated detection and quantification of aberrant transcripts with novel splicing events

The paper introduces SpliCeAT, a pipeline that detects, quantifies, and analyzes non-canonical splicing events using bulk RNA-seq data, validated with long-read sequencing.

Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

This study shows hypoxia-induced CTCF promotes EMT in breast cancer by regulating alternative splicing through chromatin looping and RNA Pol II pausing.

Alternative splicing controls pan-neuronal homeobox gene expression

The paper shows that UNC-75/CELF-mediated alternative splicing controls pan-neuronal expression of the homeobox gene ceh-44/CUX in C. elegans while excluding a Golgi-localized golgin from neurons.

PhaSeDis: A Manually Curated Database of Phase Separation-Disease Associations and Corresponding Small Molecules

PhaSeDis is a database that curates phase separation-disease associations and small molecules, expanding on MloDisDB with more entries and molecular interaction data.

The dark side of fluorescent protein tagging: the impact ofprotein tags on biomolecular condensation

This study shows that fluorescent and poly-histidine tags alter the condensation properties of Dhh1 in vitro and P-body numbers in vivo, raising concerns about the reliability of tagged protein condensation experiments.

RNA promotes synapsin phase separation providing a platform for local translation

The paper shows RNA promotes synapsin phase separation, forming condensates that organize synaptic vesicles and enhance local translation.

A hybrid model for multiscale prediction and generation of phase separating protein regions

This paper introduces Phaseek, a hybrid model for predicting and generating phase-separating protein regions, achieving 70% success in vivo peptide design.

Splicing accuracy varies across human introns, tissues and age

The paper examines mis-splicing across human introns, tissues, and age using RNA-sequencing data, finding correlations with spliceosome components and age-related neurodegenerative disease genes.

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation

The paper identifies a conserved region in LARP4 that interacts with RACK1 to enhance translation of specific mRNAs.

Differential Analysis of Alternative Splicing Events in gene regions using Residual Neural Networks

This paper introduces deepSpecas, a deep learning method for differential analysis of alternative splicing events in RNA-seq samples, achieving higher precision with reduced sensitivity.

Transcriptome-wide alternative mRNA splicing analysis reveals post-transcriptional regulation of neuronal differentiation.

The paper analyzes alternative splicing changes during neuronal differentiation in SH-SY5Y cells, identifying RNA binding proteins that regulate splicing and influence differentiation and stress response.

Structures of aberrant spliceosome intermediates on their way to disassembly

The paper reports cryo-EM structures of aberrant spliceosome intermediates in S. pombe, revealing how a helicase-protein pair maintains catalytic dormancy and facilitates disassembly.

Axon Trafficking Counteracts Aberrant Protein Aggregation in Neurons

This study identifies ANXA7 as a critical adaptor for TIA1-containing RNP retrograde transport in axons, showing that its disruption leads to TIA1 aggregation and neurodegeneration.

Bioinformatics Analysis of Non-Coding UTR Variants in STAT1 Reveals Disruption of miRNA Binding, mRNA Stability, and Oncogenic Potential

The paper identifies functional SNPs in STAT1 UTRs that disrupt miRNA binding, mRNA stability, and oncogenic potential using bioinformatics tools.

RBM10 loss induces aberrant splicing of cytoskeletal and extracellular matrix mRNAs and promotes metastatic fitness.

This study shows that RBM10 loss causes aberrant splicing of cytoskeletal and ECM genes, leading to RAC1 activation and metastatic fitness in thyroid cancer.

SMG6-dependent RNA decay maintains dsRNA homeostasis and restrains immunogenicity in hepatocellular carcinoma

This study shows that SMG6-dependent NMD prevents dsRNA accumulation and immunogenicity in HCC by maintaining dsRNA homeostasis and suppressing MHC-I-presented peptides.

The SARS-CoV-2 nucleocapsid protein inhibits the cellular Nonsense-Mediated mRNA Decay (NMD) pathway preventing the full enzymatic activation of UPF1.

This study shows that SARS-CoV-2 Np inhibits NMD by blocking UPF1 activity and disrupting UPF1/UPF2 complex formation, revealing a novel mechanism of viral evasion.

Identification and classification of abundant RNA-binding proteins in the mouse lens and interactions of Carhsp1, Igf2bp1/ZBP1, and Ybx1 with crystallin and β-actin mRNAs

The paper identifies abundant RNA-binding proteins in mouse lenses and characterizes their interactions with crystallin and β-actin mRNAs using proteomic, transcriptomic, and imaging techniques.

The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models

The paper uses large-scale deep learning models to study intron retention, showing that chromatin state plays a key role in its regulation.

Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data

The paper develops a framework to identify splice-site creating variants (SSCVs) using transcriptome data, identifies 30,130 SSCVs, and demonstrates their therapeutic potential with ASOs.

Live-cell imaging of circular and long non-coding RNAs associated to FUS pathological aggregates by Pepper fluorescent RNA

The paper uses Pepper fluorescent RNA to visualize and study the dynamics of circRNAs and lncRNAs in live cells, revealing their interactions with pathological aggregates and stress granules.

RNase III cleavage signals spread across splice junctions enforce sequential processing of co-hosted snoRNAs.

The paper identifies an RNase III cleavage signal in exon-exon junctions that ensures sequential processing of co-hosted snoRNAs in S. pombe, with conservation in animals and plants.

Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives

Halfpipe quantifies RNA half-lives from metabolic labeling RNA-seq data, showing similar half-lives for constantly expressed RNAs in mitosis and G1 phase.

Alternative splicing in 300 human cells and tissues is sparsely distributed and strongly associated with cell identity

The paper shows that alternative splicing patterns are more specific to cell identity than gene expression and are sparsely distributed across cell types.

De novo and inherited dominant variants in U4 and U6 snRNAs cause retinitis pigmentosa

The paper identifies de novo and inherited variants in U4 and U6 snRNAs causing retinitis pigmentosa and shows their impact on snRNP biogenesis.