RNA Research and Splicing

The paper identifies the role of the CCR4-NOT complex in recognizing unfolded nascent polypeptides and triggering mRNA deadenylation and decay to maintain protein quality control in yeast.

This study shows how sequence blockiness affects liquid-liquid phase separation in polypeptide-like polymers through coarse-grained simulations and mean-field theory.

The paper identifies PUM1 and PUM2 as cofactors for viral noncoding RNAs HSUR1 and HSUR2 in mRNA repression, showing PUM binding is required for productive HSUR-mRNA engagement.

This study identifies BCAS2 as a critical regulator of PDAC progression by promoting alternative splicing of weak 5' splice sites, specifically enhancing SOS1 exon 21 inclusion and RAC-signaling activation.

The paper identifies exitron-type splicing events in IDR-coding sequences across jawed vertebrates, showing donor-proximal cis control in TARDBP despite sequence divergence.

This study identifies RBFOX2 as a suppressor of oncogenic cell plasticity in Group 3 medulloblastoma by regulating alternative splicing and cytoskeletal dynamics.

This study shows that Cajal bodies in Arabidopsis roots regulate transcript retention and processing during hypoxia, affecting gene expression and stress tolerance.

The paper identifies the regulatory roles of the CCR4-NOT complex in mRNA deadenylation and decay by analyzing transcriptome-wide effects of subunit depletion.

The paper identifies post-transcriptional changes in liver tissue before morphological transformation in chemically induced cancer.

The paper identifies the Marangoni effect as a mechanism for intracellular transport of biomolecular condensates using C. elegans zygotes and in vitro experiments.

This paper introduces a sequential Design of Experiments framework to study multidimensional biomolecular condensation, revealing protein-specific interactions and context-dependent behaviors in RNA-binding condensates.

This study identifies how RNA splicing factor mutations drive myeloid neoplasm by disrupting proteomic networks through mis-splicing, validated via single-cell transcriptomics and proteomics.

This study investigates how synapsin-1 and actin form ordered nanoscale assemblies through phase separation, showing that actin scaffolds retain structural memory for condensate reformation.

The paper identifies a network of RNA-binding proteins that retain pre-mRNPs in nuclear speckles, linking splicing status to nuclear retention and speckle organization.

The paper investigates transcriptional adaptation in paralog gene families using Perturb-seq, finding six paralog pairs show adaptation and identifying mechanisms like nonsense-mediated decay and nuclear import.

The paper shows that the strength of a gene's first 5' splice site determines its expression level through intron-mediated enhancement, independent of 3' splice site strength.

This paper introduces BOB-seq, a method for isoform-resolved multiplexed RNA sequencing that uses bioorthogonal barcoding to capture full-length transcripts and improve splicing effect detection.

The paper identifies a cross-tissue splicing signature as a biomarker for ReNU syndrome, distinguishing affected individuals from controls with high specificity.

The paper identifies RNA-binding domains of Ssd1 essential for yeast tolerance to extra chromosomes, showing their role in fitness and target binding.

This study maps APA dynamics during quiescence transitions in fission yeast and identifies Pabp's role in regulating sod2 expression via APA to control cellular quiescence.

Non3nExonFinder identifies shared non-triplet coding exons across transcripts, prioritizing candidates based on CDS status and divisibility by three, with high concordance in validation.

This study investigates how sequence design parameters influence phase separation and mixing behavior of intrinsically disordered proteins (IDPs) when mixed.

This study shows that TBPL2-dependent transcription is essential for maintaining cellular organization in growing oocytes by regulating RNA stability and decay machinery.

PeakATail identifies poly(A)-sites in single-cell RNA-seq with precision, controlling error rates and validating results against curated data.

The paper uses hybrid RNA sequencing to analyze transcript isoform changes during influenza infection and interferon treatment, identifying RNA-binding proteins involved in immune remodeling.

The paper identifies cryptic last exons (CLEs) in vertebrates and shows they generate regulated, functional transcript isoforms with developmental roles.

This study shows that Angiogenin activity is essential for RNA remodeling during the maternal-to-zygotic transition in mouse embryos, affecting transcript clearance, small-RNA dynamics, and RNA granule organization.

This paper introduces a physics-based framework for simulating biomolecular phase separation and presents a machine learning library for metabolite-driven condensate formation.