RNA Research and Splicing

No evidence that human GIGYF2 interacts with growth factor receptor-bound protein 10 (GRB10): implication for human disease

The paper shows that human GIGYF2 does not interact with GRB10, challenging the current understanding of their role in disease.

Nanometer condensate organization in live cells derived from partitioning measurements

The paper quantifies microenvironment structure within cellular condensates using partitioning measurements, revealing spatial inhomogeneity and its role in macromolecular transport.

A distinct mechanism of RNA recognition by the transcription factor GATA1

This study identifies a distinct mechanism of RNA recognition by GATA1, showing competitive DNA/RNA binding through an overlapping surface involving the ARM-like domain.

Cleavage site heterogeneity at the pre-mRNA 3'-untranslated region regulates gene expression

The paper shows that heterogeneity in pre-mRNA 3'-end cleavage sites regulates gene expression, particularly in antioxidant responses, by modulating cleavage efficiency and primary site usage under oxidative stress.

Genetically-encoded phase separation sensors for intracellular probing of biomolecular condensates

The paper introduces genetically encoded LLPS-sensors for probing biomolecular condensates in mouse skin, demonstrating their tunability and effectiveness in assessing intracellular phase separation dynamics.

Molecular mechanisms of recruitment, function and regulation of UPF1 in histone mRNA decay

This study identifies the molecular interactions of UPF1 in histone mRNA decay, showing how SLBP and UPF2 regulate its unwinding activity and degradation efficiency.

Alternative splicing of transposable elements in human breast cancer

The paper examines TE-driven alternative splicing in breast cancer using long-read RNA sequencing, identifying tumor-specific splicing events and TE-derived isoforms with potential therapeutic implications.

Most Upf1-associated mRNAs have short poly(A) tails, lack a premature termination codon and are targeted by NMD.

The paper shows that most Upf1-associated mRNAs have short poly(A) tails, lack PTCs, and are targeted by NMD, redefining the pathway's scope.

The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA

The paper shows that FBF-2, a PUF RNA-binding protein, maintains stem cells even when it cannot bind RNA, indicating that RNA-binding is not essential for its biological activity.

Pumilio differentially binds to mRNA 3' UTR isoforms to regulate localization of synaptic proteins

This study shows Pumilio binds different mRNA 3' UTR isoforms to regulate synaptic protein localization in Drosophila neurons.

LUC7 proteins define two major classes of 5' splice sites in animals and plants

The paper identifies two major classes of 5' splice sites regulated by LUC7 proteins in animals and plants, showing conserved function across species.

Accurate Predictions of Phase Separating Proteins at Single Amino Acid Resolution

This paper introduces catGRANULE 2.0 ROBOT, an algorithm predicting protein LLPS at single amino acid resolution, showing high performance and experimental validation.

A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions

The paper identifies CNBP as a factor required for mRNA localization to cell protrusions by forming a motor-adaptor complex with KIF1C.

Controlled by disorder: phosphorylation modulates SRSF1 domain availability for spliceosome maturation

This study shows phosphorylation of SRSF1's RS domain modulates its interactions with RRM1 and RNA, affecting spliceosome maturation and phase separation.

Destabilisation of bam transcripts terminates the mitotic phase of Drosophila female germline differentiation

The paper shows that Bam transcript instability, regulated by Rbp9 and Rbfox1, terminates the mitotic phase of Drosophila female germline differentiation.

Multiplexed Assays of Human Disease-relevant Mutations Reveal UTR Dinucleotide Composition as a Major Determinant of RNA Stability

The paper identifies UA dinucleotides as a major determinant of RNA stability through UTR variants, linking them to disease and immune response pathways.

Mapping interactions within the NMD decapping complex reveals how Upf1 recruits Dcp2 onto mRNA targets

The paper maps interactions within the NMD decapping complex, showing how Upf1 recruits Dcp2 onto mRNA targets through domain-specific binding and competition.

Regulation of co-translational mRNA decay by PAP and DXO1 in Arabidopsis

This study investigates the regulation of co-translational mRNA decay (CTRD) in Arabidopsis, showing that PAP inhibits XRN4 and DXO1, with DXO1 specifically targeting stress-response mRNAs.

SUGP1 loss is the sole driver of SF3B1 hotspot mutant missplicing in cancer

The paper identifies SUGP1 loss as the sole driver of SF3B1 hotspot mutant missplicing in cancer, while AQR loss has an indirect effect.

Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

This study shows that Pab1 in yeast primarily controls translation by blocking mRNA decapping and decay, with reduced mRNA abundance driving translational changes.

An RNA Splicing System that Excises Transposons from Animal mRNAs

This paper describes a novel RNA splicing system, SOS splicing, that removes transposons from mRNAs in C. elegans and human cells, protecting genes from TE-mediated disruption.

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

The paper identifies SERBP1 as a protein involved in PARylation-dependent complexes that regulate splicing, cell division, and ribosome biogenesis, with implications for neurodegenerative diseases.

Decoding Biomolecular Condensate Dynamics: An Energy Landscape Approach

This paper uses an energy landscape framework to analyze how low-complexity protein sequences encode material properties of biomolecular condensates, showing periodic motifs promote elasticity and random sequences promote viscosity.

Deep learning-based prediction of tissue-specific splice sites in the human neural retina

The paper develops a retina-specific splice prediction tool based on SpliceAI to improve identification of splice sites in the human neural retina, but it does not significantly enhance predictions for tissue-specific variants or identify novel pathogenic variants.

Spatially regulated mRNA decay contributes to sharpening the even-skipped expression pattern in the Drosophila embryo

The paper shows spatially regulated mRNA decay sharpens the even-skipped expression pattern in Drosophila embryos by improving stripe definition and affecting segmentation.

Diverse mechanisms of DDX3Y suppression by DDX3X

This study shows DDX3X suppresses DDX3Y through both transcript and protein stabilization mechanisms in male cancer cells, revealing cell-type-specific cross-regulation between X- and Y-linked paralogs.

Kinetic characterization of three human DExD/H-box RNA helicases

This study develops a bioluminescence-based assay to kinetically characterize three human RNA helicases and establishes a high-throughput method for inhibitor discovery.

DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice.

This study shows DIS3L is essential for mouse embryo development but not cell viability, as its absence causes severe embryo degeneration and impaired protein synthesis without affecting cell survival or transcriptome levels.

Dynamics and Evolutionary Conservation of B Complex Protein Recruitment During Spliceosome Activation

This study uses CoSMoS to show that Prp38, Snu23, and Spp381 form a BCP subcomplex that binds to pre-mRNA after tri-snRNP and releases after NTC association, with conserved dynamics in yeast and humans.

Imp and Syp in vivo temporal RNA interactomes uncover networks of temporal regulators of Drosophila brain development.