RNA Research and Splicing

Transcriptional adaptation influences buffering among essential paralog gene families

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 strength of a gene's first 5' splice site is a key determinant of its expression

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.

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

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.

A cross-tissue splicing signature as a quantitative biomarker for ReNU syndrome

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

Domains of RNA-binding protein Ssd1 required for tolerating chromosome amplification in yeast

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

Unraveling APA dynamics during quiescence transitions reveals Pabp modulation of sod2 expression via APA to regulate cellular quiescence

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: transcript-aware identification of shared non-triplet coding exons

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

Designed IDPs phase separate and mix or demix according to sequence designed parameters

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

TBPL2-dependent transcription controls RNA stability and cellular organization in growing oocytes

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

PeakATail: precision-first poly(A)-site calling and calibrated alternative polyadenylation analysis in single-cell RNA-seq

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

Mapping global transcript isoform landscapes of influenza A virus infection and interferon stimulation reveals RNA-binding protein networks associated with immune remodeling

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.

Physiological Cryptic Last Exon Splicing Generates Regulated and Functional Transcript Isoforms Across Vertebrates

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

Angiogenin activity regulates RNA remodeling during the maternal-to-zygotic transition in early mouse embryogenesis

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.

A unified intermediate-resolution framework for modeling biomolecular condensates at near-cellular complexity

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

idTAG enables programmable and physiologically faithful control of endogenous protein degradation

The paper introduces idTAG, a system for controlled protein degradation that maintains physiological protein levels and allows programmable degradation kinetics.

Genomic Engineering of Gene Dosage: A Generalizable Framework for Modeling Haploinsufficiency-Mediated Human Disorders through Splicing Modulation

This paper introduces a framework to model haploinsufficiency-mediated human disorders by modulating gene dosage through splicing, demonstrating its application in creating accurate animal models for cardiomyopathies.

ZNF121 recruits YTHDF2 to modulate mRNA stability

The paper identifies ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA decay by facilitating its binding to target transcripts, thereby modulating mRNA stability and cell-cycle regulation.

Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research

The paper provides a uniformly processed compendium of alternative splicing profiles from pediatric cancer and non-diseased tissues, enabling large-scale analysis of splicing aberrations in pediatric cancers.

Reprogramming mRNA localization by targeted RNA-protein interference reveals roles in oncogenesis

This study uses CRISPR/dCas13 to interfere with RNA-RBP interactions, showing that disrupting mRNA localization reduces cancer cell invasiveness and metastasis.

Introns encode a vast new class of Kink-loop RNAs that autoregulate pre-mRNA splicing

The paper identifies a new class of intron-derived Kink-loop RNAs (klRNAs) that autoregulate pre-mRNA splicing in humans and mice.

A human transcriptomic deletion links cortical expansion and cancer

The paper identifies a human-specific transcriptomic deletion in HMMR that affects cell division plasticity and links cortical expansion to cancer risk.

GLOBAL ANALYSIS OF PROTRUSION-TRANCSRIPTOMES IDENTIFIES DISTINCT CATEGORIES OF LOCALIZED RNAS IN NON-NEURONAL CELLS

The paper develops a fractionation workflow to study RNA localization in non-neuronal cells and identifies six categories of protrusion-localized RNAs, including long non-coding RNAs and pseudogenes.

NAT10 supports CAG repeat-associated mRNA stabilization and is associated with hepatic metabolic reprogramming during spaceflight

This study identifies NAT10 as a regulator of CAG repeat-containing mRNA stability and links its upregulation in spaceflight to metabolic reprogramming in mouse liver.

Protein expression is amplified by stabilizing mRNA using gene-specific antisense oligonucleotides

The paper demonstrates that antisense oligonucleotides (ASOs) can upregulate gene expression by stabilizing mRNA through targeting destabilizing elements like PREs, with therapeutic implications for haploinsufficiency disorders.

Spatiotemporal isoform profiling identifies a central activator of microexon splicing in C. elegans

The paper identifies RBM-25 as a central activator of microexon splicing in C. elegans through spatiotemporal isoform profiling and genetic screening.

Size Control of hnRNPK-based Nucleolar Condensates by RNA-Regulated Fusion Dynamics

This study identifies how RNA-regulated fusion dynamics of hnRNPK-based nucleolar condensates prevent coalescence and maintain size control.

Beyond codon optimality: codon pairs regulate mRNA stability dependent on translation

The paper identifies codon pairs and amino acid pairs as regulators of mRNA stability in zebrafish, showing context-dependent decay mechanisms involving deadenylation and decapping.

Distinct genetic architectures of mRNA expression and splicing QTL in the Diversity Outbred mouse population

The paper maps eQTL, isoQTL, irQTL, and sQTL in DO mice, showing distinct genetic effects on mRNA expression and splicing, and identifies candidate genes and regulatory mechanisms.

An intersectional expression platform for gene complementation using RNA-fragment end joining (REJ)

This paper introduces an RNA-fragment end joining (REJ) platform for gene complementation that enables precise and efficient splicing of RNA units into functional mRNAs.

Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence

The paper presents a single-cell long-read isoform atlas across 26 human tissues, revealing novel isoforms and their role in cellular identity and senescence.