Emerging evidence suggests that intron-detaining transcripts (IDTs) are a nucleus-detained and polyadenylated mRNA pool for cell to quickly and effectively respond to environmental stimuli and stress. However, the underlying mechanisms of detained intron (DI) splicing are still largely unknown. Here, we suggest that post-transcriptional DI splicing is paused at the Bact state, an active spliceosome but not catalytically primed, which depends on Smad Nuclear Interacting Protein 1 (SNIP1) and RNPS1 (a serine-rich RNA binding protein) interaction. RNPS1 and Bact components preferentially dock at DIs and the RNPS1 docking is sufficient to trigger spliceosome pausing. Haploinsufficiency of Snip1 attenuates neurodegeneration and globally rescues IDT accumulation caused by a previously reported mutant U2 snRNA, a basal spliceosomal component. Snip1 conditional knockout in the cerebellum decreases DI splicing efficiency and causes neurodegeneration. Therefore, we suggest that SNIP1 and RNPS1 form a molecular brake to promote spliceosome pausing, and that its misregulation contributes to neurodegeneration.
Spliceosomes/metabolism* ; Introns/genetics* ; RNA Splicing ; RNA, Messenger/genetics* ; Cell Nucleus/metabolism*

Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.
Animals ; Alternative Splicing/genetics* ; RNA Splicing ; Spliceosomes/metabolism* ; RNA, Messenger/metabolism* ; Communicable Diseases/genetics* ; Mammals/metabolism*

Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell "housekeeping" machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
Humans ; Neoplasms/metabolism* ; RNA Precursors/metabolism* ; RNA Splicing ; RNA Splicing Factors/metabolism* ; Spliceosomes/metabolism*

As novel somatic mutations, spliceosome mutations have been identified in recent years with the advent of whole exone/genome sequencing technology in hematopoietic malignancy. These new findings provide another view to understand these diseases other than DNA methylation, chromatin modification, transcription regulation, DNA repair and signal transduction. In this review, the structure as well as function of spliceosome are introduced and the common mutations such as SF3B1, U2AF35, SRSF2 and ZRSR2 as well as their frequency, mutation versions, clinical phenotypies and effects on prognosis are discussed.
DNA Methylation ; DNA Repair ; Hematologic Neoplasms ; genetics ; Humans ; Mutation ; Myelodysplastic Syndromes ; Prognosis ; Signal Transduction ; Spliceosomes ; genetics

PURPOSE: Heterochromatin protein 1gamma (HP1gamma) interacts with chromosomes by binding to lysine 9-methylated histone H3 or DNA/RNA. HP1gamma is involved in various biological processes. The purpose of this study is to gain an understanding of how HP1gamma functions in these processes by identifying HP1gamma-binding proteins using mass spectrometry. MATERIALS AND METHODS: We performed affinity purification of HP1gamma-binding proteins using G1/S phase or prometaphase HEK293T cell lysates that transiently express mock or FLAG-HP1gamma. Coomassie staining was performed for HP1gamma-binding complexes, using cell lysates prepared by affinity chromatography FLAG-agarose beads, and the bands were digested and then analyzed using a mass spectrometry. RESULTS: We identified 99 HP1gamma-binding proteins with diverse cellular functions, including spliceosome, regulation of the actin cytoskeleton, tight junction, pathogenic Escherichia coli infection, mammalian target of rapamycin signaling pathway, nucleotide excision repair, DNA replication, homologous recombination, and mismatch repair. CONCLUSION: Our results suggested that HP1gamma is functionally active in DNA damage response via protein-protein interaction.
Actin Cytoskeleton ; Biological Processes ; Chromatography, Affinity ; DNA Damage* ; DNA Mismatch Repair ; DNA Repair ; DNA Replication ; DNA* ; Escherichia coli Infections ; Heterochromatin* ; Histones ; Homologous Recombination ; Lysine ; Mass Spectrometry ; Prometaphase ; Sirolimus ; Spliceosomes ; Tight Junctions

OBJECTIVETo identify the MPL L391-V392ins12 spliceosome and analyze its frequencies in patients with myeloproliferative neoplasms (MPN).

METHODSMPL aberrant spliceosome was identified through reverse transcription polymerase chain reaction (RT-PCR)combined with cloning sequencing. The mutation of this spliceosome in 248 MPN patients and 200 normal people was determined by allele-specific polymerase chain reaction (AS-PCR).

RESULTSA novel aberrant spliceosome of MPL gene (MPL L391-V392ins12)was identified, i.e. 36 bp intron was retained between exon7 and exon8, and there were 12 amino acids (EGLKLLPADIPV)inserted. MPL L391-V392ins12 mutation was detected in 19 (7.66%)of the 248 patients with MPN, including 1 (1.92%) of 52 patients with PV, 14 (9.66%) of 145 with ET, and 4 (7.84%) of 51 with PMF. And the mutation was not detected in the group of 200 normal people.

CONCLUSIONMPL L391-V392ins12 spliceosome is an aberrant spliceosome present in the MPN. It can be detected in PV, ET and PMF, and more frequently in ET and PMF. This mutation may play an important role in the process of MPN.

Humans ; Mutation ; Myeloproliferative Disorders ; genetics ; Neoplasms ; genetics ; Polymerase Chain Reaction ; Receptors, Thrombopoietin ; genetics ; Spliceosomes

Hematologic Neoplasms ; genetics ; Humans ; Mutation ; RNA ; genetics ; RNA Splicing ; Spliceosomes ; genetics

Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.
Animals ; Base Sequence ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotides ; metabolism ; Oocytes ; cytology ; metabolism ; Pseudouridine ; metabolism ; RNA Precursors ; metabolism ; RNA Splice Sites ; RNA Splicing ; RNA, Messenger ; genetics ; metabolism ; RNA, Small Nuclear ; genetics ; metabolism ; Ribonucleoproteins, Small Nuclear ; genetics ; metabolism ; Saccharomyces cerevisiae ; genetics ; metabolism ; Saccharomyces cerevisiae Proteins ; genetics ; metabolism ; Spliceosomes ; genetics ; metabolism ; Uridine ; analogs & derivatives ; metabolism ; Xenopus ; genetics ; metabolism

Little is known about pre-mRNA splicing in Dictyostelium discoideum although its genome has been completely sequenced. Our analysis suggests that pre-mRNA splicing plays an important role in D. discoideum gene expression as two thirds of its genes contain at least one intron. Ongoing curation of the genome to date has revealed 40 genes in D. discoideum with clear evidence of alternative splicing, supporting the existence of alternative splicing in this unicellular organism. We identified 160 candidate U2-type spliceosomal proteins and related factors in D. discoideum based on 264 known human genes involved in splicing. Spliceosomal small ribonucleoproteins (snRNPs), PRP19 complex proteins and late-acting proteins are highly conserved in D. discoideum and throughout the metazoa. In non-snRNP and hnRNP families, D. discoideum orthologs are closer to those in A. thaliana, D. melanogaster and H. sapiens than to their counterparts in S. cerevisiae. Several splicing regulators, including SR proteins and CUG-binding proteins, were found in D. discoideum, but not in yeast. Our comprehensive catalog of spliceosomal proteins provides useful information for future studies of splicing in D. discoideum where the efficient genetic and biochemical manipulation will also further our general understanding of pre-mRNA splicing.
Alternative Splicing ; Animals ; Arabidopsis ; genetics ; Dictyostelium ; genetics ; Drosophila melanogaster ; genetics ; Genome, Protozoan ; Humans ; Phylogeny ; Ribonucleoproteins, Small Nuclear ; classification ; genetics ; Saccharomyces cerevisiae ; genetics ; Spliceosomes ; genetics ; metabolism

The aim of this study was to explore the effect of 2 different spliceosomes of X-box binding protein 1 (XBP-1), the spliced form XBP-1s and unspliced form XBP-1u, on myeloma cell differentiation and its mechanism. The overexpression plasmids pcDNA3.1-C-XBP1u and pcDNA3.1-C-XBP1s were constructed and transfected into myeloma cell line U266, RPMI8226. The morphology of U266 and RPMI 8226 cells was observed by means of light microscope, the expression rate of CD49e on cell surface was detected by flow cytometry, the ELISA was used to determine the changes of light chain protein level in supernatants of cell culture, the Western blot was used to assay the expression changes of XBP1u and XBP1s. The results showed that the overexpression of XBP1u could promote the myeloma cell differentiation morphologically displaying the maturation of plasmocytes, the CD49e positive expression rates on surface of U266 and RPMI8226 cells were obviously up-regulated from 9.02±0.3% and 5.17±0.92% in control group to 27.7±1.14% and 13.97±1.79% respectively (p<0.01), the levels of light chain protein in supernatants of U266 and RPMI 8226 cell cultures increased from 474.75±19.52 ng/ml and 289.44±6.19 ng/ml in control group to 692.34±21.17 ng/ml and 401.55±13.7 ng/ml respectively (p<0.01, p<0.05), while the above-mentioned parameters in the overexpressed XBP-1s showed no significant changes, which indicated no promotive effect of overexpressed XBP1s on myeloma cell differentiation. It is concluded that the up-regulation of XBP-1u expression plays an important role in the differentiation of myeloma cells.
Cell Differentiation ; genetics ; Cell Line, Tumor ; DNA-Binding Proteins ; genetics ; Gene Expression Regulation, Neoplastic ; Humans ; Multiple Myeloma ; genetics ; pathology ; Regulatory Factor X Transcription Factors ; Spliceosomes ; genetics ; Transcription Factors ; genetics ; Transfection ; X-Box Binding Protein 1