| 2001 |
SPF30 (SMNDC1) is a nuclear protein that associates with both U4/U5/U6 tri-snRNP and U2 snRNP components. In the absence of SPF30, the preformed tri-snRNP fails to assemble into the spliceosome. GST-SPF30 pull-down from HeLa nuclear extract associated most strongly with U4/U6-90 and core Sm and tri-snRNP proteins, establishing SPF30 as an essential factor for docking the U4/U5/U6 tri-snRNP to the A complex during spliceosome assembly. |
Immunodepletion of SPF30 from HeLa nuclear extract (splicing assay), GST pull-down with mass spectrometric identification of co-purified proteins, nuclear localization confirmed |
The Journal of biological chemistry |
High |
11331295
|
| 2008 |
SPF30 bridges the prespliceosome and tri-snRNP: (1) the central Tudor domain of SPF30 interacts with the C-terminal tails of SmD1, SmD3, and Lsm4; (2) the N-terminal domain of SPF30 interacts with U2AF35 (a prespliceosome 3′-splice-site recognition factor); (3) the C-terminus of SPF30 interacts with the middle domain of hPrp3 (a U4/U6 di-snRNP/tri-snRNP component). The U2AF35 and hPrp3 interactions can occur simultaneously, linking 3′ splice site recognition to tri-snRNP addition. |
Co-immunoprecipitation and GST pull-down mapping experiments with domain-deletion constructs of SPF30 and its partners |
The Journal of biological chemistry |
Medium |
18211889
|
| 2011 |
The Tudor domain of SPF30 recognizes symmetrically and asymmetrically dimethylated arginine (DMA) through an aromatic cage that mediates cation-π interactions. Solution NMR structures of the SPF30 Tudor domain bound to DMA-containing peptides show that binding is independent of residues proximal to the dimethylarginine in the ligand, but is enhanced by cooperativity when multiple methylation marks are presented in RGG-rich peptide ligands. SPF30 is the weaker DMA binder compared with SMN. |
NMR solution structures of Tudor domain–DMA peptide complexes, isothermal titration calorimetry, site-directed mutagenesis |
Nature structural & molecular biology |
High |
22101937 22363433
|
| 2012 |
Quantitative binding characterization showed that SPF30's Tudor domain is the weakest methyl-arginine binder among SMN, TDRD3, and SPF30, recognizing only GAR (glycine-arginine-rich) motif sequences, and does not efficiently bind non-GAR arginine-containing sequences. SPF30 Tudor domain binds both symmetrical and asymmetrical DMA but with lower affinity than SMN. |
Fluorescence polarization and ITC binding assays with a peptide library; crystal structures of TDRD3 Tudor domain used comparatively |
PloS one |
Medium |
22363433
|
| 2009 |
Fission yeast Spf30 (ortholog of SMNDC1) is required for exosome-mediated heterochromatin silencing at centromeres. Spf30 colocalizes with the exosome RNase Dis3 at centromeric heterochromatin; Dis3 helps recruit Spf30. Loss of Spf30 phenocopies the dis3-54 mutant: reduced silencing and accumulation of polyadenylated centromeric transcripts without loss of siRNA production. Spf30 binds centromeric transcripts and localizes to centromeres in an RNA-dependent manner. |
Genetic epistasis (double mutant analysis), chromatin immunoprecipitation (ChIP), RNA immunoprecipitation, fluorescence localization studies in S. pombe |
Molecular and cellular biology |
Medium |
20028739
|
| 2021 |
SPF30 associates with the MTR4-exosome RNA-decay machinery. The interaction between SPF30 and the exosome core is mediated by MTR4 and RRP6. The N- and C-terminal regions of SPF30 (not the Tudor domain) mediate association with MTR4 and the exosome. SPF30 knockdown caused subtle delay in 12S pre-rRNA processing to mature 5.8S rRNA. Shotgun proteomics of the SPF30 interactome linked it to ribosome biogenesis, pre-mRNA splicing, and box C/D snoRNA biogenesis. The SPF30–MTR4 interaction is regulated by ATP hydrolysis of AAA-ATPase NVL2. |
Co-immunoprecipitation, domain-deletion mapping, shotgun proteomics (interactome), siRNA knockdown with rRNA processing assay |
The international journal of biochemistry & cell biology |
Medium |
33422691
|
| 2022 |
Knockdown of Smndc1 in a murine α-cell line triggers global repression of α-cell gene-expression programs and upregulation of β-cell markers, including the transcription factor Pdx1. Mechanistically, Smndc1 loss modulates the activities of the BAF and Atrx chromatin remodeling complexes to derepress Pdx1 expression, linking SMNDC1 function to control of both splicing and chromatin remodeling in pancreatic islet cell identity. The repressive role of SMNDC1 is conserved in human pancreatic islets. |
RNAi screen, siRNA knockdown, transcriptomic analysis, chromatin remodeling complex activity assays (BAF/ATRX), human islet knockdown experiments with insulin secretion and PDX1 expression readouts |
Cell reports |
Medium |
36044849
|
| 2023 |
SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction, and can be recapitulated in vitro. Small-molecule inhibitors targeting the dimethylarginine-binding pocket of the SMNDC1 Tudor domain drastically alter protein-protein interactions and subcellular localization, and cause splicing changes for SMNDC1-dependent genes. |
Live-cell fluorescence imaging, in vitro phase-separation assay, small-molecule Tudor domain inhibitors, proteomics of inhibitor-treated cells, splicing assays |
Nature communications |
High |
37587144
|
| 2024 |
A poison exon in Smndc1 (within intron 2) is conserved across mammals and plants and mediates autoregulatory control of SMNDC1 protein levels via nonsense-mediated mRNA decay (NMD). Mice and A. thaliana lacking this poison exon show deregulated SMNDC1 protein levels, pervasive alterations in mRNA processing, and organismal size restriction, demonstrating that this autoregulatory mechanism is functionally important in vivo. |
Mouse and Arabidopsis genetic models with poison-exon deletion, RT-PCR for NMD-targeted transcripts, mRNA processing analysis, organismal growth phenotyping |
PLoS genetics |
High |
39150991
|
| 2025 |
SPF30 autoregulates its own expression through a negative feedback mechanism: increased SPF30 promotes inclusion of a cassette exon (intron 2) and/or generation of an exon 4a splice variant, both of which are degraded by NMD, reducing SPF30 mRNA levels. Exon 4a inclusion contributes more than cassette exon inclusion to adjusting SPF30 levels. The C-terminal region of SPF30 (including the latter part of an α-helix and a kink-like structure) is required for binding to RNA containing exon 4a and for the autoregulatory mechanism. A short sequence within exon 4 of SPF30 mRNA is required for exon 4a inclusion. |
In vivo splicing assays with deletion constructs, siRNA knockdown and overexpression of SPF30, RT-PCR quantification of splice variants, RNA-binding domain mapping by mutagenesis |
bioRxivpreprint |
Medium |
bio_10.1101_2025.03.04.641417
|