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1.
Nucleic Acids Res ; 52(7): 4037-4052, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38499487

ABSTRACT

Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3' splice site usage. Together, our results highlight the role of the 3'-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.


Subject(s)
DEAD-box RNA Helicases , RNA Splicing Factors , RNA, Small Nuclear , RNA-Binding Proteins , Ribonucleoproteins, Small Nuclear , Spliceosomes , Spliceosomes/metabolism , Spliceosomes/genetics , Ribonucleoproteins, Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/chemistry , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/chemistry , Humans , RNA, Small Nuclear/metabolism , RNA, Small Nuclear/genetics , RNA, Small Nuclear/chemistry , DEAD-box RNA Helicases/metabolism , DEAD-box RNA Helicases/genetics , RNA Splicing , Introns/genetics , HeLa Cells , Protein Binding , Coiled Bodies/metabolism , HEK293 Cells
2.
Genetics ; 226(1)2024 Jan 03.
Article in English | MEDLINE | ID: mdl-37982586

ABSTRACT

Methylphosphate Capping Enzyme (MePCE) monomethylates the gamma phosphate at the 5' end of the 7SK noncoding RNA, a modification thought to protect 7SK from degradation. 7SK serves as a scaffold for assembly of a snRNP complex that inhibits transcription by sequestering the positive elongation factor P-TEFb. While much is known about the biochemical activity of MePCE in vitro, little is known about its functions in vivo, or what roles-if any-there are for regions outside the conserved methyltransferase domain. Here, we investigated the role of Bin3, the Drosophila ortholog of MePCE, and its conserved functional domains in Drosophila development. We found that bin3 mutant females had strongly reduced rates of egg-laying, which was rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 promotes fecundity by repressing P-TEFb. bin3 mutants also exhibited neuromuscular defects, analogous to a patient with MePCE haploinsufficiency. These defects were also rescued by genetic reduction of P-TEFb activity, suggesting that Bin3 and MePCE have conserved roles in promoting neuromuscular function by repressing P-TEFb. Unexpectedly, we found that a Bin3 catalytic mutant (Bin3Y795A) could still bind and stabilize 7SK and rescue all bin3 mutant phenotypes, indicating that Bin3 catalytic activity is dispensable for 7SK stability and snRNP function in vivo. Finally, we identified a metazoan-specific motif (MSM) outside of the methyltransferase domain and generated mutant flies lacking this motif (Bin3ΔMSM). Bin3ΔMSM mutant flies exhibited some-but not all-bin3 mutant phenotypes, suggesting that the MSM is required for a 7SK-independent, tissue-specific function of Bin3.


Subject(s)
Drosophila melanogaster , Methyltransferases , Animals , Female , Humans , Drosophila/genetics , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , HeLa Cells , Methyltransferases/genetics , Methyltransferases/metabolism , Positive Transcriptional Elongation Factor B/genetics , Positive Transcriptional Elongation Factor B/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , RNA, Small Nuclear/genetics
3.
Int J Mol Sci ; 24(21)2023 Oct 25.
Article in English | MEDLINE | ID: mdl-37958537

ABSTRACT

The survival motor neuron (SMN) complex is a multi-megadalton complex involved in post-transcriptional gene expression in eukaryotes via promotion of the biogenesis of uridine-rich small nuclear ribonucleoproteins (UsnRNPs). The functional center of the complex is formed from the SMN/Gemin2 subunit. By binding the pentameric ring made up of the Sm proteins SmD1/D2/E/F/G and allowing for their transfer to a uridine-rich short nuclear RNA (UsnRNA), the Gemin2 protein in particular is crucial for the selectivity of the Sm core assembly. It is well established that post-translational modifications control UsnRNP biogenesis. In our work presented here, we emphasize the crucial role of Gemin2, showing that the phospho-status of Gemin2 influences the capacity of the SMN complex to condense in Cajal bodies (CBs) in vivo. Additionally, we define Gemin2 as a novel and particular binding partner and phosphorylation substrate of the mTOR pathway kinase ribosomal protein S6 kinase beta-1 (p70S6K). Experiments using size exclusion chromatography further demonstrated that the Gemin2 protein functions as a connecting element between the 6S complex and the SMN complex. As a result, p70S6K knockdown lowered the number of CBs, which in turn inhibited in vivo UsnRNP synthesis. In summary, these findings reveal a unique regulatory mechanism of UsnRNP biogenesis.


Subject(s)
RNA-Binding Proteins , Ribosomal Protein S6 Kinases, 70-kDa , Cyclic AMP Response Element-Binding Protein/metabolism , Phosphorylation , Ribonucleoproteins, Small Nuclear/genetics , Ribosomal Protein S6 Kinases, 70-kDa/metabolism , RNA-Binding Proteins/metabolism , SMN Complex Proteins/genetics , Uridine/metabolism
4.
Nucleic Acids Res ; 51(20): 10970-10991, 2023 11 10.
Article in English | MEDLINE | ID: mdl-37811895

ABSTRACT

P-TEFb and CDK12 facilitate transcriptional elongation by RNA polymerase II. Given the prominence of both kinases in cancer, gaining a better understanding of their interplay could inform the design of novel anti-cancer strategies. While down-regulation of DNA repair genes in CDK12-targeted cancer cells is being explored therapeutically, little is known about mechanisms and significance of transcriptional induction upon inhibition of CDK12. We show that selective targeting of CDK12 in colon cancer-derived cells activates P-TEFb via its release from the inhibitory 7SK snRNP. In turn, P-TEFb stimulates Pol II pause release at thousands of genes, most of which become newly dependent on P-TEFb. Amongst the induced genes are those stimulated by hallmark pathways in cancer, including p53 and NF-κB. Consequently, CDK12-inhibited cancer cells exhibit hypersensitivity to inhibitors of P-TEFb. While blocking P-TEFb triggers their apoptosis in a p53-dependent manner, it impedes cell proliferation irrespective of p53 by preventing induction of genes downstream of the DNA damage-induced NF-κB signaling. In summary, stimulation of Pol II pause release at the signal-responsive genes underlies the functional dependence of CDK12-inhibited cancer cells on P-TEFb. Our study establishes the mechanistic underpinning for combinatorial targeting of CDK12 with either P-TEFb or the induced oncogenic pathways in cancer.


Subject(s)
Positive Transcriptional Elongation Factor B , RNA Polymerase II , Neoplasms/genetics , NF-kappa B/genetics , NF-kappa B/metabolism , Positive Transcriptional Elongation Factor B/genetics , Positive Transcriptional Elongation Factor B/metabolism , Ribonucleoproteins, Small Nuclear/genetics , RNA Polymerase II/genetics , RNA Polymerase II/metabolism , RNA-Binding Proteins/metabolism , Tumor Suppressor Protein p53/genetics , Humans , Cell Line, Tumor
5.
Biol Pharm Bull ; 46(7): 1010-1014, 2023.
Article in English | MEDLINE | ID: mdl-37394631

ABSTRACT

Recently, the finding of recurrent mutations in the spliceosome components in cancer has indicated that the spliceosome is a potential target for cancer therapy. However, the number of small molecules known to affect the cellular spliceosome is currently limited probably because of the lack of a robust cell-based approach to identify small molecules that target the spliceosome. We have previously reported the development of a genetic reporter to detect the cellular levels of small nuclear ribonucleoproteins (snRNPs), which are subunits of the spliceosome, using a split luciferase. However, the original protocol was designed for small scale experiments and was not suitable for compound screening. Here, we found that the use of cell lysis buffer used in blue native polyacrylamide gel electrophoresis (BN-PAGE) dramatically improved the sensitivity and the robustness of the assay. Improved assay conditions were used to discover a small molecule that altered the reporter activity. Our method may be used with other cellular macromolecular complexes and may assist in the discovery of small bioactive molecules.


Subject(s)
RNA Splicing , Ribonucleoproteins , Ribonucleoproteins/genetics , Ribonucleoproteins/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , Spliceosomes/metabolism , Luciferases/genetics
6.
BMC Womens Health ; 23(1): 396, 2023 07 28.
Article in English | MEDLINE | ID: mdl-37507701

ABSTRACT

BACKGROUND: Basal-like breast cancer (BLBC) takes up about 10-20% of all breast cancer(BC), what's more, BLBC has the lowest survival rate among all BC subtypes because of lacks of efficient treatment methods. We aimed to explore the molecules that can be used as diagnostic maker for BLBC at early stage and provide optimized treatment strategies for BLBC patients in this study. METHODS: Apply weighted gene co-expression network analysis (WGCNA) to identify gene modules related to BLBC;The functional enrichment of candidate genes related to BLBC in the red module of Go data package and KEGG analysis;Overlapping cross analysis of URGs and WGCNA to identify candidate genes in each BC subtype;Divide BCBL patients into high-risk and low-risk groups, and analyze the two groups of overall survival (OS) and relapse free survival (RFS);Screening of GEMIN4 dependent cell lines; QRT PCR was used to verify the expression of GEMIN4 transfected with siRNA; CCK8 was used to determine the effect of GEMIN4 on cell viability; Positive cell count detected by BrdU staining;GO and KEGG enrichment analysis of GEMIN4. RESULTS: The "red module" has the highest correlation with BLBC, with 913 promising candidate genes identified from the red module;913 red module candidate genes related to BLBC participated in multiple GO terms, and KEGG enrichment analysis results mainly enriched in estrogen signaling pathways and pathways in cancer;There are 386 overlapping candidate genes among the 913 "red module" genes identified by 1893 common URG and WGCNA;In BLBC patients, 9 highly expressed genes are associated with OS. Five highly expressed genes are associated with RFS. Kaplan Meier survival analysis suggests that high GEMIN4 expression levels are associated with poor prognosis in BLBC patients;The GEMIN4 gene dependency score in HCC1143 and CAL120 cell lines is negative and low; Si-GEMIN4-1 can significantly reduce the mRNA expression of GEMIN4; Si-GEMIN4 can inhibit cell viability; Si-GEMIN4 can reduce the number of positive cells;GO enrichment analysis showed that GEMIN4 is associated with DNA metabolism processes and adenylate binding; KEGG pathway enrichment analysis shows that GEMIN4 is related to ribosome biogenesis in eukaryotes. CONCLUSION: We hypothesized that GEMIN4 may be the potential target for the treatment of BLBC.


Subject(s)
Breast Neoplasms , Humans , Female , Breast Neoplasms/drug therapy , Neoplasm Recurrence, Local , Gene Expression Profiling/methods , Signal Transduction , Minor Histocompatibility Antigens/therapeutic use , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism
7.
Int J Mol Sci ; 24(14)2023 Jul 19.
Article in English | MEDLINE | ID: mdl-37511433

ABSTRACT

N-acetylglucosamine kinase (NAGK) has been identified as an anchor protein that facilitates neurodevelopment with its non-canonical structural role. Similarly, small nuclear ribonucleoprotein polypeptide N (SNRPN) regulates neurodevelopment and cognitive ability. In our previous study, we revealed the interaction between NAGK and SNRPN in the neuron. However, the precise role in neurodevelopment is elusive. In this study, we investigate the role of NAGK and SNRPN in the axodendritic development of neurons. NAGK and SNRPN interaction is significantly increased in neurons at the crucial stages of neurodevelopment. Furthermore, overexpression of the NAGK and SNRPN proteins increases axodendritic branching and neuronal complexity, whereas the knockdown inhibits neurodevelopment. We also observe the interaction of NAGK and SNRPN with the dynein light-chain roadblock type 1 (DYNLRB1) protein variably during neurodevelopment, revealing the microtubule-associated delivery of the complex. Interestingly, NAGK and SNRPN proteins rescued impaired axodendritic development in an SNRPN depletion model of Prader-Willi syndrome (PWS) patient-derived induced pluripotent stem cell neurons. Taken together, these findings are crucial in developing therapeutic approaches for neurodegenerative diseases.


Subject(s)
Prader-Willi Syndrome , Ribonucleoproteins, Small Nuclear , Humans , Autoantigens/metabolism , Chromosomes, Human, Pair 15/metabolism , Cytoplasmic Dyneins/metabolism , Dyneins/metabolism , Microtubules/metabolism , Neurons/metabolism , Peptides/metabolism , Ribonucleoproteins, Small Nuclear/genetics , snRNP Core Proteins
8.
Hum Mol Genet ; 32(19): 2901-2912, 2023 09 16.
Article in English | MEDLINE | ID: mdl-37440454

ABSTRACT

Telomere biology disorders (TBDs) are characterized by short telomeres, premature aging, bone marrow failure and cancer predisposition. Germline mutations in NHP2, encoding for one component of the telomerase cofactor H/ACA RNA binding complex together with Dyskerin, NOP10 and GAR1, have been previously reported in rare cases of TBDs. Here, we report two novel NHP2 variants (NHP2-A39T and NHP2-T44M) identified in a compound heterozygous patient affected by premature aging, bone marrow failure/myelodysplastic syndrome and gastric cancer. Although still able to support cell viability, both variants reduce the levels of hTR, the telomerase RNA component, and telomerase activity, expanding the panel of NHP2 pathological variants. Furthermore, both variants fail to be incorporated in the H/ACA RNA binding complex when in competition with wild-type endogenous NHP2, and the lack of incorporation causes their drastic proteasomal degradation. By RoseTTAFold prediction followed by molecular dynamics simulations, we reveal a dramatic distortion of residues 33-41, which normally position on top of the NHP2 core, as the main defect of NHP2-A39T, and high flexibility and the misplacement of the N-terminal region (residues 1-24) in NHP2-T44M and, to a lower degree, in NHP2-A39T. Because deletion of amino acids 2-24 causes a reduction in NHP2 levels only in the presence of wild-type NHP2, while deletion of amino acids 2-38 completely disrupts NHP2 stability, we propose that the two variants are mis-incorporated into the H/ACA binding complex due to the altered dynamics of the first 23 amino acids and/or the distortion of the residues 25-41 loop.


Subject(s)
Aging, Premature , Telomerase , Humans , Telomerase/genetics , Ribonucleoproteins, Small Nuclear/genetics , RNA/genetics , RNA/metabolism , Bone Marrow Failure Disorders , Protein Stability , Telomere/metabolism , Nuclear Proteins/genetics
9.
Acta Neuropathol ; 146(3): 477-498, 2023 09.
Article in English | MEDLINE | ID: mdl-37369805

ABSTRACT

GEMIN5 is essential for core assembly of small nuclear Ribonucleoproteins (snRNPs), the building blocks of spliceosome formation. Loss-of-function mutations in GEMIN5 lead to a neurodevelopmental syndrome among patients presenting with developmental delay, motor dysfunction, and cerebellar atrophy by perturbing SMN complex protein expression and assembly. Currently, molecular determinants of GEMIN5-mediated disease have yet to be explored. Here, we identified SMN as a genetic suppressor of GEMIN5-mediated neurodegeneration in vivo. We discovered that an increase in SMN expression by either SMN gene therapy replacement or the antisense oligonucleotide (ASO), Nusinersen, significantly upregulated the endogenous levels of GEMIN5 in mammalian cells and mutant GEMIN5-derived iPSC neurons. Further, we identified a strong functional association between the expression patterns of SMN and GEMIN5 in patient Spinal Muscular Atrophy (SMA)-derived motor neurons harboring loss-of-function mutations in the SMN gene. Interestingly, SMN binds to the C-terminus of GEMIN5 and requires the Tudor domain for GEMIN5 binding and expression regulation. Finally, we show that SMN upregulation ameliorates defective snRNP biogenesis and alternative splicing defects caused by loss of GEMIN5 in iPSC neurons and in vivo. Collectively, these studies indicate that SMN acts as a regulator of GEMIN5 expression and neuropathologies.


Subject(s)
Muscular Atrophy, Spinal , RNA-Binding Proteins , Humans , Motor Neurons/metabolism , Muscular Atrophy, Spinal/genetics , Muscular Atrophy, Spinal/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/chemistry , Ribonucleoproteins, Small Nuclear/metabolism , RNA-Binding Proteins/metabolism , SMN Complex Proteins/genetics , Tudor Domain
10.
Oncogene ; 42(22): 1821-1831, 2023 06.
Article in English | MEDLINE | ID: mdl-37041411

ABSTRACT

Prostate cancer is the most commonly diagnosed noncutaneous cancer in American men. TDRD1, a germ cell-specific gene, is erroneously expressed in more than half of prostate tumors, but its role in prostate cancer development remains elusive. In this study, we identified a PRMT5-TDRD1 signaling axis that regulates the proliferation of prostate cancer cells. PRMT5 is a protein arginine methyltransferase essential for small nuclear ribonucleoprotein (snRNP) biogenesis. Methylation of Sm proteins by PRMT5 is a critical initiation step for assembling snRNPs in the cytoplasm, and the final snRNP assembly takes place in Cajal bodies in the nucleus. By mass spectrum analysis, we found that TDRD1 interacts with multiple subunits of the snRNP biogenesis machinery. In the cytoplasm, TDRD1 interacts with methylated Sm proteins in a PRMT5-dependent manner. In the nucleus, TDRD1 interacts with Coilin, the scaffold protein of Cajal bodies. Ablation of TDRD1 in prostate cancer cells disrupted the integrity of Cajal bodies, affected the snRNP biogenesis, and reduced cell proliferation. Taken together, this study represents the first characterization of TDRD1 functions in prostate cancer development and suggests TDRD1 as a potential therapeutic target for prostate cancer treatment.


Subject(s)
Prostatic Neoplasms , Ribonucleoproteins, Small Nuclear , Male , Humans , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/analysis , Ribonucleoproteins, Small Nuclear/metabolism , Testis/metabolism , Cell Nucleus/metabolism , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Cell Proliferation/genetics , HeLa Cells , Protein-Arginine N-Methyltransferases/genetics , Protein-Arginine N-Methyltransferases/metabolism , Cell Cycle Proteins/metabolism
11.
Int J Mol Sci ; 24(6)2023 Mar 09.
Article in English | MEDLINE | ID: mdl-36982311

ABSTRACT

The formation of mature mRNA requires cutting introns and splicing exons. The occurrence of splicing involves the participation of the spliceosome. Common spliceosomes mainly include five snRNPs: U1, U2, U4/U6, and U5. SF3a2, an essential component of spliceosome U2 snRNP, participates in splicing a series of genes. There is no definition of SF3a2 in plants. The paper elaborated on SF3a2s from a series of plants through protein sequence similarity. We constructed the evolutionary relationship of SF3a2s in plants. Moreover, we analyzed the similarities and differences in gene structure, protein structure, the cis-element of the promoter, and expression pattern; we predicted their interacting proteins and constructed their collinearity. We have preliminarily analyzed SF3a2s in plants and clarified the evolutionary relationship between different species; these studies can better serve for in-depth research on the members of the spliceosome in plants.


Subject(s)
Ribonucleoproteins, Small Nuclear , Spliceosomes , Spliceosomes/metabolism , Phylogeny , Ribonucleoproteins, Small Nuclear/genetics , RNA Splicing/genetics , Ribonucleoprotein, U2 Small Nuclear/chemistry , Ribonucleoprotein, U2 Small Nuclear/genetics , Ribonucleoprotein, U2 Small Nuclear/metabolism , RNA, Messenger/metabolism
13.
Biol Pharm Bull ; 46(2): 147-157, 2023.
Article in English | MEDLINE | ID: mdl-36724942

ABSTRACT

Intron recognition by the spliceosome mainly depends on conserved intronic sequences such as 5' splice sites, 3' splice sites, and branch sites. Therefore, even substitution of just a single nucleotide in a 5' or 3' splice site abolishes the splicing at the mutated site and leads to cryptic splice site usage. A number of disease-causative mutations have been found in 5' and 3' splice sites, but the genes with these mutations still maintain the correct protein-coding sequence, so recovery of splicing at the mutated splice site may produce a normal protein. Mutations in the spliceosome components have been shown to change the balance between the conformational transition and disassembly of the spliceosome, which affects the decision about whether the reaction of the incorporated substrate will proceed. In addition, the lower disassembly rate caused by such mutations induces splicing of the mutated splice site. We hypothesized that small compounds targeting the spliceosome may include a compound mimicking the effect of those mutations. Thus, we screened a small-compound library and identified a compound, BAY61-3606, that changed the cellular small nuclear ribonucleoprotein composition and also showed activity of enhancing splicing at the mutated 3' splice site of the reporter gene, as well as splicing at the suboptimal 3' splice site of endogenous cassette exons. These results indicate that further analysis of the mechanism of action of BAY61-3606 could enable modulation of the fidelity of splicing.


Subject(s)
RNA Splice Sites , Spliceosomes , RNA Splice Sites/genetics , Spliceosomes/genetics , Spliceosomes/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , Niacinamide , Mutation
14.
J Cell Sci ; 136(2)2023 01 15.
Article in English | MEDLINE | ID: mdl-36620952

ABSTRACT

SART3 is a multifunctional protein that acts in several steps of gene expression, including assembly and recycling of the spliceosomal U4/U6 small nuclear ribonucleoprotein particle (snRNP). In this work, we provide evidence that SART3 associates via its N-terminal HAT domain with the 12S U2 snRNP. Further analysis showed that SART3 associates with the post-splicing complex containing U2 and U5 snRNP components. In addition, we observed an interaction between SART3 and the RNA helicase DHX15, which disassembles post-splicing complexes. Based on our data, we propose a model that SART3 associates via its N-terminal HAT domain with the post-splicing complex, where it interacts with U6 snRNA to protect it and to initiate U6 snRNA recycling before a next round of splicing.


Subject(s)
RNA Splicing , Spliceosomes , RNA Splicing/genetics , Spliceosomes/genetics , Spliceosomes/metabolism , RNA, Small Nuclear/genetics , RNA, Small Nuclear/metabolism , Ribonucleoprotein, U4-U6 Small Nuclear/genetics , Ribonucleoprotein, U4-U6 Small Nuclear/metabolism , Ribonucleoprotein, U5 Small Nuclear/genetics , Ribonucleoprotein, U5 Small Nuclear/metabolism , Ribonucleoprotein, U2 Small Nuclear/genetics , Ribonucleoprotein, U2 Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism
15.
Nucleic Acids Res ; 51(2): 712-727, 2023 01 25.
Article in English | MEDLINE | ID: mdl-36537210

ABSTRACT

Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3'-extended snRNA transcripts in patients' cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.


Subject(s)
Ribonucleoproteins, Small Nuclear , Spliceosomes , Spliceosomes/genetics , Spliceosomes/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Mutation , Introns/genetics , RNA Splicing/genetics , RNA, Small Nuclear/metabolism , Homeostasis/genetics
16.
Cell Chem Biol ; 29(12): 1709-1720.e7, 2022 12 15.
Article in English | MEDLINE | ID: mdl-36476517

ABSTRACT

RNA granules are cytoplasmic condensates that organize biochemical and signaling complexes in response to cellular stress. Functional proteomic investigations under RNA-granule-inducing conditions are needed to identify protein sites involved in coupling stress response with ribonucleoprotein regulation. Here, we apply chemical proteomics using sulfonyl-triazole (SuTEx) probes to capture cellular responses to oxidative and nutrient stress. The stress-responsive tyrosine and lysine sites detected mapped to known proteins involved in processing body (PB) and stress granule (SG) pathways, including LSM14A, FUS, and Enhancer of mRNA-decapping protein 3 (EDC3). Notably, disruption of EDC3 tyrosine 475 (Y475) resulted in hypo-phosphorylation at S161 and S131 and altered protein-protein interactions (PPIs) with decapping complex components (DDX6, DCP1A/B) and 14-3-3 proteins. This resulting mutant form of EDC3 was capable of rescuing the PB-deficient phenotype of EDC3 knockout cells. Taken together, our findings identify Y475 as an arsenic-responsive site that regulates RNA granule formation by coupling EDC3 post-translational modification and PPI states.


Subject(s)
Proteomics , Ribonucleoproteins, Small Nuclear , Ribonucleoproteins, Small Nuclear/chemistry , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , Tyrosine , Biomolecular Condensates , RNA, Messenger/metabolism
17.
Nucleic Acids Res ; 50(20): 11834-11857, 2022 11 11.
Article in English | MEDLINE | ID: mdl-36321655

ABSTRACT

The spliceosome undergoes extensive rearrangements as it assembles onto precursor messenger RNAs. In the earliest assembly step, U1snRNA identifies the 5' splice site. However, U1snRNA leaves the spliceosome relatively early in assembly, and 5' splice site identity is subsequently maintained through interactions with U6snRNA, protein factor PRP8, and other components during the rearrangements that build the catalytic site. Using a forward genetic screen in Caenorhabditis elegans, we have identified suppressors of a locomotion defect caused by a 5'ss mutation. Here we report three new suppressor alleles from this screen, two in PRP8 and one in SNRNP200/BRR2. mRNASeq studies of these suppressor strains indicate that they also affect specific native alternative 5'ss, especially for suppressor PRP8 D1549N. A strong suppressor at the unstructured N-terminus of SNRNP200, N18K, indicates a novel role for this region. By examining distinct changes in the splicing of native genes, examining double mutants between suppressors, comparing these new suppressors to previously identified splicing suppressors from yeast, and mapping conserved suppressor residues onto cryoEM structural models of assembling human spliceosomes, we conclude that there are multiple interactions at multiple stages in spliceosome assembly responsible for maintaining the initial 5'ss identified by U1snRNA for entry into the catalytic core.


Subject(s)
RNA Splice Sites , RNA Splicing Factors , Spliceosomes , Animals , Humans , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Caenorhabditis elegans Proteins/genetics , Caenorhabditis elegans Proteins/metabolism , Mutation , Ribonucleoprotein, U5 Small Nuclear/genetics , Ribonucleoprotein, U5 Small Nuclear/metabolism , Ribonucleoproteins, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , RNA Precursors/genetics , RNA Precursors/metabolism , RNA Splicing , RNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/genetics , Spliceosomes/genetics , Spliceosomes/metabolism , RNA Splicing Factors/genetics
18.
Int J Mol Sci ; 23(21)2022 Nov 02.
Article in English | MEDLINE | ID: mdl-36362191

ABSTRACT

SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3' splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and non-redundant roles of SLU7 as an integrative hub of different levels of gene expression regulation, including epigenetic DNA remodeling, modulation of transcription and protein stability. Here we review those findings, the multiple factors and mechanisms implicated as well as the cellular functions affected. For instance, SLU7 is essential to secure liver differentiation, genome integrity acting at different levels and a correct cell cycle progression. Accordingly, the aberrant expression of SLU7 could be associated with human diseases including cancer, although strikingly, it is an essential survival factor for cancer cells. Finally, we discuss the implications of SLU7 in pathophysiology, with particular emphasis on the progression of liver disease and its possible role as a therapeutic target in human cancer.


Subject(s)
RNA Splicing , Ribonucleoproteins, Small Nuclear , Humans , Ribonucleoproteins, Small Nuclear/genetics , RNA Splicing Factors/genetics , RNA Splice Sites , Epigenesis, Genetic , Protein Stability , Alternative Splicing
19.
BMJ Open Ophthalmol ; 7(1)2022 08.
Article in English | MEDLINE | ID: mdl-36161854

ABSTRACT

BACKGROUND: Large databases permit quantitative description of genes in terms of intolerance to loss of function ('haploinsufficiency') and prevalence of missense variants. We explored these parameters in inherited retinal disease (IRD) genes. METHODS: IRD genes (from the 'RetNet' resource) were classified by probability of loss of function intolerance (pLI) using online Genome Aggregation Database (gnomAD) and DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) databases. Genes were identified having pLI ≥0.9 together with one or both of the following: upper bound of CI <0.35 for observed to expected (o/e) ratio of loss of function variants in the gnomAD resource; haploinsufficiency score <10 in the DECIPHER resource. IRD genes in which missense variants appeared under-represented or over-represented (Z score for o/e ratio of <-2.99 or >2.99, respectively) were also identified. The genes were evaluated in the gene ontology Protein Analysis THrough Evolutionary Relationships (PANTHER) resource. RESULTS: Of 280 analysed genes, 39 (13.9%) were predicted loss of function intolerant. A greater proportion of X-linked than autosomal IRD genes fulfilled these criteria, as expected. Most autosomal genes were associated with dominant disease. PANTHER analysis showed >100 fold enrichment of spliceosome tri-snRNP complex assembly. Most encoded proteins were longer than the median length in the UniProt database. Fourteen genes (11 of which were in the 'haploinsufficient' group) showed under-representation of missense variants. Six genes (SAMD11, ALMS1, WFS1, RP1L1, KCNV2, ADAMTS18) showed over-representation of missense variants. CONCLUSION: A minority of IRD-associated genes appear to be 'haploinsufficient'. Over-representation of spliceosome pathways was observed. When interpreting genetic tests, variants found in genes with over-representation of missense variants should be interpreted with caution.


Subject(s)
Potassium Channels, Voltage-Gated , Retinal Diseases , ADAMTS Proteins/genetics , Eye Proteins/genetics , Genomics , Humans , Mutation , Potassium Channels, Voltage-Gated/genetics , Retina/metabolism , Retinal Diseases/genetics , Ribonucleoproteins, Small Nuclear/genetics
20.
Am J Med Genet A ; 188(10): 2932-2940, 2022 10.
Article in English | MEDLINE | ID: mdl-35861185

ABSTRACT

Pathogenic variants in GEMIN4 have recently been linked to an inherited autosomal recessive neurodevelopmental disorder characterized with microcephaly, cataracts, and renal abnormalities (NEDMCR syndrome). This report provides a retrospective review of 16 patients from 11 unrelated Saudi consanguineous families with GEMIN4 mutations. The cohort comprises 11 new and unpublished clinical details from five previously described patients. Only two missense, homozygous, pathogenic variants were found in all affected patients, suggesting a founder effect. All patients shared global developmental delay with variable ophthalmological, renal, and skeletal manifestations. In addition, we knocked down endogenous Drosophila GEMIN4 in neurons to further investigate the mechanism of the functional defects in affected patients. Our fly model findings demonstrated developmental defects and motor dysfunction suggesting that loss of GEMIN4 function is detrimental in vivo; likely similar to human patients. To date, this study presents the largest cohort of patients affected with GEMIN4 mutations. Considering that identifying GEMIN4 defects in patients presenting with neurodevelopmental delay and congenital cataract will help in early diagnosis, appropriate management and prevention plans that can be made for affected families.


Subject(s)
Abnormalities, Multiple , Cataract , Microcephaly , Neurodevelopmental Disorders , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Cataract/pathology , Homozygote , Humans , Kidney/abnormalities , Microcephaly/diagnosis , Microcephaly/genetics , Microcephaly/pathology , Minor Histocompatibility Antigens , Neurodevelopmental Disorders/genetics , Pedigree , Ribonucleoproteins, Small Nuclear/genetics , Syndrome , Urogenital Abnormalities
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