RNA Research and Splicing

Stress Changes the Material State of a Bacterial Biomolecular Condensate and Shifts its Function from mRNA Decay to Storage

The paper shows stress causes bacterial BR-bodies to switch from mRNA decay to storage by changing their physical state and function.

Cell-Type-Resolved Isoform Atlas of Human Tissues Reveals Age and Alzheimer's Disease-Associated Splicing Changes

The paper introduces Sciege, a method to estimate cell type-specific isoform distributions using bulk and single-cell RNA-seq data, revealing age and Alzheimer's disease-related splicing changes.

Localized control of protein phase separation via membrane binding

This study investigates how membrane binding influences 2D versus 3D phase separation of the protein FUS, showing that membrane binding allows 2D condensates to form at lower concentrations than bulk phase separation.

Chemical inhibition of Exon Junction Complex assembly impairs mRNA localization and neural stem cells ciliogenesis

This study shows that inhibiting EJC assembly with EJC-i disrupts mRNA localization and neural stem cell ciliogenesis by affecting multiple post-transcriptional processes.

A Deep Dive into Statistical Modeling of RNA Splicing QTLs Reveals New Variants that Explain Neurodegenerative Disease

The paper improves sQTL modeling by incorporating alternative splicing representation and introduces MAJIQTL, finding new sQTLs linked to Alzheimer's disease.

Cytoplasmic roles of HSATIII RNAs in RNA granule assembly and production of actin cytoskeleton-associated repeat-containing proteins

This study identifies cytoplasmic roles of HSATIII RNAs in forming RNA granules and producing proteins during thermal stress recovery.

Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity

The paper identifies DDX55 as a novel regulator of 3'UTR isoform diversity through integrative analysis of RNA binding protein depletion experiments.

Cell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC cortical organoids

The paper develops an integrative sequencing strategy to catalog NRXN1 isoforms across human brain tissues and hiPSC organoids, revealing cell-type-specific splicing patterns and therapeutic potential of ASO targeting.

Targeted RNAi screen reveals novel regulators of RNA-binding protein phase transitions in Caenorhabditis elegans oocytes

The paper identifies six novel regulators of RNA-binding protein phase transitions in C. elegans oocytes through a targeted RNAi screen.

RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint

The paper investigates the role of RNA splicing factors in abscission checkpoint maintenance and identifies a unique RNA landscape associated with ACB formation.

Alternative Splicing And Global Transcriptome Changes Associated With LPS Stimulation In Human Peripheral Blood Mononuclear Cells

This study examines alternative splicing and transcriptome changes in human PBMCs after LPS stimulation, identifying novel pathways and splicing events involved in inflammation.

Control of gene output by intron RNA structure

This study investigates how intron RNA structure affects gene expression using reporter assays and machine learning, finding that base pairing significantly modulates mRNA and protein levels.

Deciphering the molecular mechanisms of FET fusion oncoprotein-DNA hollow co-condensates

This study investigates FUS-ERG fusion oncoprotein-DNA co-condensates, revealing nested asymmetric phase separation and their potential for DNA-based information manipulation.

The ORB2 RNA-binding protein negatively regulates its target transcripts during the Drosophila maternal-to-zygotic transition via its functionally conserved Zinc binding 'ZZ' domain

This study identifies ORB2 as a regulator of maternal mRNAs during the Drosophila MZT, showing its ZZ domain mediates repression through interactions with post-transcriptional regulators.

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

The paper introduces SPICE, a framework that uses splicing assays and generative design to create cell-specific gene regulation elements for research and therapy.

Origins and Implications of Intron Retention Quantitative Trait Loci in Human Tissues

The paper identifies intron retention quantitative trait loci (irQTLs) in human tissues and shows their association with GWAS traits and eQTLs, revealing shared genetic regulation and potential NMD effects.

Phosphorylation-dependent tuning of mRNA deadenylation rates

The paper shows phosphorylation modulates deadenylation rates via multivalent interactions in RNA adaptors, enabling graded regulation of mRNA decay.

Do 5' regions of human protein-coding genes contain the blueprints for alternative splicing?

The paper investigates whether 5' regions of human protein-coding genes contain blueprints for alternative splicing by comparing genes with multiple and single transcript isoforms.

Refractive index as an indicator for dynamic protein condensation in cell nuclei

This study uses refractive index mapping to detect dynamic protein condensation in cell nuclei, showing it is sensitive to reversible condensation and reveals differences from fluorescence-based methods.

RNA Binding of GAPDH Controls Transcript Stability and Protein Translation in Acute Myeloid Leukemia

The paper identifies GAPDH as a non-canonical RNA-binding protein in AML that stabilizes transcripts and promotes translation, revealing its role in tumor proliferation.

A kinetic ruler controls mRNA poly(A) tail length

The paper identifies a kinetic ruler mechanism where Nab2 protein concentration determines mRNA poly(A) tail length through competition between polyadenylation and RNA-binding.

DUX4-induced HSATII RNA accumulation drives protein aggregation impacting RNA processing pathways.

The paper shows DUX4 induces HSATII RNA accumulation, leading to protein aggregation and disruption of RNA processing pathways in muscle cells.

Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing

The paper uses long-read RNA-seq and isoLASER to distinguish cis- and trans-directed splicing events in human and mouse data, identifying thousands of cis-regulated events in disease-relevant genes.

Glucocorticoids Modulate mRNA Translation Fate Through P-Body Dynamics

This study shows glucocorticoids increase P-body numbers and alter mRNA translation fate based on transcript sequence features, not abundance.

CaMKII-RNMT axis directs activity-dependent control of RNA dynamics in neurons

This study identifies the CaMKII-RNMT axis as a mechanism controlling activity-dependent RNA dynamics and neuronal morphogenesis through phosphorylation and degradation of RNMT.

Control of 3' Splice Site Selection in S. cerevisiae by a Highly Conserved Amino Acid within the Prp8 α-finger Domain

This study shows that a specific amino acid in the Prp8 protein influences 3' splice site selection in yeast by interacting with the -3 pyrimidine of the 3SS, affecting splicing efficiency and 3SS competition.

Real-time tracking of mRNP complex assembly reveals various mechanisms that synergistically enhance translation repression

The paper uses single-molecule fluorescence microscopy to study mRNP assembly mechanisms in translation repression, revealing synergistic roles of RNA-binding proteins.

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

This paper identifies a conserved unstructured region in Prp40 WW domains that facilitates their positioning to promote non-canonical intron splicing in yeast.

Arabidopsis DXO1 is an evolutionarily diverged homolog that impacts ribosome loading and mRNA surveillance

This study identifies Arabidopsis DXO1 as a diverged ortholog involved in 5'-end RNA quality control, ribosome loading, and mRNA surveillance through its serine-rich N-terminal domain.

Selective RNA sequestration in biomolecular condensates directs cell fate transitions

The paper profiles RNA content in P-bodies across vertebrate species, showing that RNA sequestration in condensates is linked to cell fate transitions through miRNA-dependent mechanisms.