RNA Research and Splicing

The paper identifies how TTC5 recruits SCAPER to initiate tubulin mRNA degradation via interaction with the CCR4-NOT complex, linking ribosome-associated mRNA decay to microtubule regulation.

This study shows that Dcp2 regulates mRNA abundance and translation to adjust metabolism and filamentation in response to nutrient availability in yeast.

This study shows cytoplasmic polyadenylation via CPEBs originated in the animal stem lineage and is conserved across cnidarians, ctenophores, and vertebrates.

The paper shows that inhibiting NMD in FSHD leads to widespread production of truncated RNA-binding proteins, some of which are toxic and can be detected in patient samples.

This study identifies HNRNPH1 as a key regulator of RBM3 expression through cold-induced exon skipping, offering potential therapeutic targets for neuroprotection.

The paper identifies post-transcriptional regulators in budding yeast by analyzing protein fragments and their effects on mRNA, revealing modular domains and interactions involved in mRNA regulation.

This paper introduces TLC-CLIP, a method to profile RNA-protein interactions with increased sensitivity and efficiency by improving CLIP library preparation.

The paper introduces HyperTRIBE, an antibody-free method to identify RNA-binding protein targets in yeast by using RNA editing, and successfully applies it to two RBPs.

The paper identifies splicing variants in modern and archaic humans using functional assays and shows differences in purifying selection and adaptive introgression.

The paper identifies a targeted degradation pathway for nascent proteins from PTC-containing mRNAs, showing CNOT4's role in coupling NMD with protein quality control.

The paper identifies cell-type specific splicing quantitative trait loci (sQTLs) in iPSCs and HLCs and shows they contribute to lipid level variation beyond what is captured by gene expression alone.

The paper compares TRIBE and STAMP methods for identifying RNA binding protein targets in human and Drosophila cells, finding TRIBE more effective in Drosophila.

This study identifies a network of DZF proteins that regulate alternative splicing through dsRNA binding and reveals their roles in splicing fidelity and cassette exon regulation.

The paper introduces PPE, a method for discovering RNA-binding proteomes in plants, identifying 1,169 RBPs including 496 novel ones and 374 RNA-binding domains.

The paper introduces Skipper, a CLIP-seq analysis tool that improves binding site detection and identifies genetic variation depletion in translation factor binding sites.

The paper uses machine learning to analyze Neanderthal and Denisovan genomes, identifying splicing variants and their potential impact on phenotypic differences.

RNAcontacts detects RNA-RNA contacts from proximity ligation assays using a two-pass alignment approach to improve sensitivity and specificity.

This study identifies NRDE2 and CCDC174 as RNA-binding proteins that enhance splicing of weak 5' splice sites by directly interacting with U1 snRNA in mouse ES cells.

This study identifies recursive splice sites in human introns using intron lariats, showing their prevalence and role in alternative exon exclusion across vertebrates.

The paper introduces an improved FISH probe labeling method that enables high-purity, low-cost probes with high labeling efficiency, applied to visualize retained introns in cells.

This study identifies PRRC2B as an RNA binding protein that regulates translation of specific mRNAs, including cell cycle regulators, and inhibits cell proliferation by affecting G1/S phase transition.

The paper identifies a mechanism called Mito-ENCay that limits MMF1 mRNA expression by targeting it to mitochondria and triggering quality control processes.

The paper investigates how different PUM1 mutations lead to distinct phenotypes by analyzing PUM1 interactomes and showing that dosage sensitivity involves non-linear mechanisms.

RCRUNCH improves eCLIP data analysis to identify RNA-binding protein binding sites and motifs, creating a comprehensive resource of in vivo-bound RBP sequence motifs.

The paper characterizes RNA-binding protein landscapes in mouse organs using ex vivo eRIC, identifying over 1300 RBPs, many not previously found in cultured cells.

This study identifies that the Rous sarcoma virus Gag polyprotein forms biomolecular condensates driven by intrinsically disordered regions, which are involved in viral assembly.

Insplico quantifies intron splicing order using short and long RNA-seq reads, revealing conserved patterns and novel features across species and tissues.

The paper extends a hiCLIP atlas of Staufen1-bound duplexes by 10-fold using computational methods and reveals structural features of RNA binding and their impact on RNA metabolism.

The paper introduces SAI-10k-calc, a tool that extends SpliceAI to predict splicing aberrations and their effects, achieving high sensitivity and specificity for variant impact prediction.