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*

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

Alternative splicing of pre-mRNA is an important mechanism for regulating gene function at the post-transcription level and for producing proteomic diversity in higher eukaryotes. The alternative splicing is regulated by the interaction between diverse cis-acting elements and trans-acting factors. Alternative splicing events of oncogenes, tumor suppressor genes and metastasis suppressor genes are associated with the initiation and development of human neoplasms. The protein isoforms sourced from alternative splicing take part in regulating the gene transcription, cell cycle, apoptosis of cells, and playing a role in tumor growth. It is possible for molecular therapy to target directly isoforms of protein produced by alternative splicing or to interfere with the process of alternative splicing.
Alternative Splicing ; genetics ; Humans ; Neoplasms ; genetics ; RNA Precursors ; metabolism ; RNA, Neoplasm ; analysis ; Transcription, Genetic

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*

OBJECTIVETo establish a minigene model of neural cell adhesion molecule L1 (NCAM L1) gene and to study its splicing patterns in different cell lines.

METHODSUsing human genetic cDNA as template, the NCAM L1 minigene fragment was amplified and inserted into eukaryotic expression vector. The minigene was transfected into 4 cell lines and the splicing patterns of NCAM L1 minigene in these cell lines were studied.

RESULTSThe splicing patterns of NCAM L1 minigene were different in individual cell lines. In PFSK and Hela cell lines, two splicied isoforms were generated but in COS-1 and R28 cell lines, only one isoform existed.

CONCLUSIONNCAM L1 minigene model can be used in alternative splicing analysis.

Cell Line ; Genetic Vectors ; Humans ; Neural Cell Adhesion Molecule L1 ; genetics ; Plasmids ; genetics ; RNA Splicing ; Transfection

OBJECTIVETo study a family affected with osteogenesis imperfecta for potential mutations in COL1A1 gene.

METHODSClinical data of an affected family was collected. Potential mutation of the COL1A1 gene was screened using polymerase chain reaction and direct sequencing. Suspected mutation was detected in 20 unaffected relatives and 200 unrelated healthy controls.

RESULTSAnalysis of RNA splicing has revealed a c.3208G/A mutation, which created a new splice sites and led to a frameshift mutation. The same mutation was not detected in the unaffected relatives or the 200 healthy controls.

CONCLUSIONMutations of the COL1A1 gene are one of the major causes of osteogenesis imperfecta in Chinese population. Our finding has enriched the mutation spectrum of type I collagen genes.

Adult ; Child, Preschool ; Collagen Type I ; genetics ; Female ; Humans ; Male ; Mutation ; Osteogenesis Imperfecta ; genetics ; RNA Splicing

OBJECTIVE: To study the correlation of splicing mutations at the 5' end of the DMD gene with their phenotypes. METHODS: DMD gene mutations were analyzed using Multiplex Ligation Probe Amplification (MLPA) and Sanger sequencing. Co-segregation analysis was performed for the pedigrees of the probands. Influence of mutations on protein function was predicted by bioinformatic analysis. RESULTS: Three novel splicing mutations were identified in three patients with different phenotypes. Patient 1 carried a c.31+3insT mutation and presented primarily with dilated cardiomyopathy (XLDC). There was no clinical signs of skeletal myopathy. Bioinformatic analysis predicted that the mutation may inactivate the splicing donor of intron 1 and lead to premature termination of protein translation. Patient 2 carried a c.264_264+4delTGTAA mutation, which led to loss of splicing donor site for intron 4, and manifested Becker muscular dystrophy (BMD). The mutation was predicted to result in skipping of exon 4. The defective protein may still retain most of its function. Patient 3 had Duchenne muscular dystrophy (DMD) and carried a c.832-3C>T mutation which was predicted to decrease the activity of splicing acceptor of intron 8, resulting in usage of alternative acceptor site or retain of intron 8. All related transcripts may cause premature termination of protein translation and complete loss of protein function. The three mutations were all inherited from the mothers of the patients. CONCLUSION Three novel splicing mutations were discovered at the 5' end of DMD gene in three patients with different disease phenotypes. Our study may facilitate understanding of the influence of splicing mutations at the 5' end of the DMD gene on dystrophin function and the correlation between genotypes and phenotypes.
Dystrophin ; genetics ; Humans ; Muscular Dystrophy, Duchenne ; genetics ; Mutation ; Phenotype ; RNA Splicing

OBJECTIVE: To explore the effect of rare synonymous variants of the ATP7B gene on the splicing of its precursor mRNA. METHODS: A total of 248 rare synonymous variants with allelic frequency of <0.005 were retrieved from the ExAc database. Human Splicing Finder (HSF) was used to predict their effect on the splicing of precursor mRNA. And ESE Finder 3.0 was used to predict the effect of such variants on the binding ability of SR protein family. Rare synonymous variants affecting the binding of two or more SR proteins were selected and verified with an in vitro mini gene splicing report system. RESULTS: HSF analysis indicated that 136 of the 248 rare synonymous variants may destroy the exonic splicing enhancer (ESE) motif. Analysis using ESE Finder 3.0 indicated that 19 of them may affect the binding of two or more SR proteins at the same time. In vitro mini gene experiment confirmed that the c.1620C>T (p.L540L) and c.3888C>T (p.A1296A) variants could lead to abnormal splicing of the corresponding exons, resulting in complete skipping of exon 4 and 25% increase in the skipping of exon 18, respectively. CONCLUSION Synonymous variants may affect the splicing of precursor mRNA in various ways, particularly the destruction of ESE motif. This study confirmed that the c.1620C>T (p.L540L) and c.3888C>T (p.A1296A) variants can affect the mRNA splicing of the ATP7B gene, resulting in skipping of corresponding exons, which may provide a basis for genetic diagnosis and consultation of carriers.
Alternative Splicing ; Copper-Transporting ATPases/genetics* ; Enhancer Elements, Genetic ; Exons ; Gene Frequency ; Humans ; RNA, Messenger/genetics*

OBJECTIVE: To detect the expression of different transcripts of lactamase β（LACTB) gene in leukemic cell lines. METHODS: NCBI website and DNAstar software were used to detect the Bioinformatics analysis of LACTB. The expression of different transcripts of LACTB gene in leukemic cell lines (THP-1, HL60, K562, U937, Jurkat and Raji) was detected by reverse transcription PCR (RT-PCR), DNA and clone sequencing; the expression of different transcripts of LACTB gene in leukemic cell lines was detected by Quantitative Real-time PCR. RESULTS: There were a variety of splicing isomers in LACTB, and it could produce a variety of protein isomers with conserved N-terminal and different C-terminal, moreover, there were many splice isoforms of LACTB in leukemia cell lines, and there were different expression patterns in different cell lines, including XR1, V1, V2 and V3. The expression of total LACTB showed high in HL60 cells, while low in Raji cells, and the difference was statistically significant (P<0.05). The V1 was high expression in U937 cells but low in Raji cells, and the difference was statistically significant (P<0.05). V2 was high expression in HL60 cells but lowly in Raji cells, and the difference was statistically significant (P<0.05). The expression of V3 was low in THP-1 cells, which was significantly different as compared with that in normal bone marrow (P<0.05). CONCLUSION The reaserch found that there are many splice isomers of LACTB in leukemic cell lines, and there are different expression patterns in different cell lines.
Alternative Splicing ; HL-60 Cells ; Humans ; Leukemia/genetics* ; Membrane Proteins/genetics* ; Mitochondrial Proteins/genetics* ; RNA Splicing ; U937 Cells ; beta-Lactamases/genetics*

OBJECTIVE: To analyze the clinical phenotype and genetic variants in five Chinese pedigrees affected with Dysferlinopathy. METHODS: Next generation sequencing (NGS) was carried out for the probands from the five pedigrees. Suspected variants were validated by Sanger sequencing. Pathogenicity of the variants was assessed based on the standards and guidelines by the American College of Medical Genetics and Genomics (ACMG). RESULTS: Ten DYSF gene variants (including 5 frameshift variants, 3 splicing variants, 1 missense variant and 1 nonsense variant) were detected. Among these, c.1375dupA (p.Met459Asnfs*15), c.610C>T (p.Arg204X), c.1180+5G>A and c.1284+2T>C were known to be pathogenic, while c.4008_4010delCCTinsAC (p.Leu1337Argfs*8), c.1137_1169del (p.379_390del), c.754A>G(p.Thr252Ala), c.1175_1176insGCAGAGTG (p.Met394Serfs*7), c.3114_3115insCGGC (p.Arg1040Profs*74) and c.1053+3G>C were unreported previously. Of the six novel variants, c.1137_1169del, c.1175_1176insGCAGAGTG and c.3114_3115insCGGC were predicted as pathogenic (PVS1+PM2+PM3), c.4008_4010delCCTinsAC as likely pathogenic (PVS1+PM2), c.754A>G and c.1053+3G>C as variants of uncertain significance based on the ACMG standards and guidelines. CONCLUSION Variants of the DYSF gene probably underlay Dysferlinopathy in the patients among the five pedigrees. Above finding has enriched the spectrum of DYSF gene variants.
Humans ; Muscular Dystrophies, Limb-Girdle/genetics* ; Mutation ; Pedigree ; Phenotype ; RNA Splicing