Alternative Splicing ; Computational Biology ; Humans ; Organ Specificity

Flowering is a critical transitional stage during plant growth and development, and is closely related to seed production and crop yield. The flowering transition is regulated by complex genetic networks, whereas many flowering-related genes generate multiple transcripts through alternative splicing to regulate flowering time. This paper summarizes the molecular mechanisms of alternative splicing in regulating plant flowering from several perspectives, future research directions are also envisioned.
Alternative Splicing/genetics* ; Arabidopsis/metabolism* ; Arabidopsis Proteins/genetics* ; Flowers/genetics*

Dilated cardiomyopathy (DCM) is a significant contributor to heart failure and can lead to life-threatening cardiovascular events at any stage. RNA-binding motif protein 20 (RBM20) gene mutation is known to be one of the causes of DCM. This mutation exhibits familial aggregation and is associated with arrhythmias, increasing the risk of sudden and early death. This article delves into the characteristics of the RBM20 gene, highlighting its role in regulating alternative splicing of the TTN gene and calcium/calmodulin-dependent protein kinase type II gene. Furthermore, the article provides a summary of treatment options available for DCM caused by RBM20 gene mutations, aiming to enhance clinicians' understanding of the RBM20 gene and provide new ideas for precision medicine treatment.
Humans ; Alternative Splicing ; Cardiomyopathy, Dilated/metabolism* ; Heart Failure/metabolism* ; Mutation

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*

To analyze the expression of splicing factors in gastric cancer using bioinformatics methods and investigate the effect of aberrantly expressed serine/arginine-rich splicing factor(SRSF10)on the phenotype of gastric cancer cells. The RNA-seq data of gastric cancer and paracancerous tissues were downloaded from The Cancer Genome Atlas(TCGA)cancer database,and bioinformatics analysis was performed to obtain the splicing factors differentially expressed in gastric cancer.The splicing factor SRSF10 was selected to investigate its effect on the development of gastric cancer.RNA interference technology was used to construct SRSF10 knockdown gastric cancer cells.MTS,Transwell,and cell scratches were used to study the effect of SRSF10 knockdown on gastric cancer cell phenotype. A total of 48 splicing factors were identified in gastric cancer by a series of bioinformatics techniques,of which 35 were up-regulated and 13 were down-regulated.The splicing factor SRSF10,which was up-regulated,was selected for further study.It was found that the gastric cancer cells after SRSF10 knockdown proliferated more slowly and had lower migration ability than normal gastric cancer cells. Multiple splicing factors are found in gastric cancer and may play an important role in the development of gastric cancer.The splicing factor SRSF10 may contribute to the pathogenesis of gastric cancer.
Alternative Splicing ; Cell Cycle Proteins ; Computational Biology ; Gene Expression Regulation, Neoplastic ; Humans ; RNA Splicing Factors ; Repressor Proteins ; Serine-Arginine Splicing Factors ; Stomach Neoplasms

The common gamma chain (gammac) is the central signaling unit for a number of cytokine receptors collectively known as the gammac cytokine receptor family. gammac is critical for ligand binding and signaling by gammac cytokines. gammac cytokine signaling had been thought to be mainly regulated by cytokine-specific receptor alpha chain expression levels with little or no effect by gammac surface levels because gammac expression was presumed to remain unchanged during T-cell activation and development. The extent of gammac cytokine responses is thought to be regulated by cytokine specific receptor subunits and not by the gammac receptor. In contrast to this prevailing view, we have recently reported that gammac itself actively regulates gammac cytokine responses. Interestingly, gammac exerted its regulatory effects not only as a conventional membrane receptor protein but also as a secreted protein whose expression was upregulated upon T-cell stimulation. Here we will review how a soluble form of gammac, which is generated by alternative splicing, regulates gammac cytokine signaling and plays a role in controlling immune activation related to autoimmune disease.
Alternative Splicing ; Autoimmune Diseases* ; Cytokines ; Humans ; Membranes ; Receptors, Cytokine ; T-Lymphocytes

PURPOSE: Alternative splicing of CD44 and aberrant levels of soluble CD44 (sCD44) protein in the serum of cancer patients has been correlated to tumor progression and metastasis. The purpose of this study was to evaluate the concentrations, and the prognostic potential of sCD44s, sCD44v5 and sCD44v6, in patients with gastric cancer. MATERIALS AND METHODS: The serum levels of sCD44s, sCD44v5 and sCD44v6 were determined quantitatively using an enzyme-linked immunosorbent assay. Serum samples were obtained from 116 patients with gastric cancer, both before and after surgery, and from 30 healthy controls. RESULTS: The serum sCD44v6 levels were significantly higher in patients with gastric cancer than in the healthy controls, whereas those of sCD44s and sCD44v5 were no different. The surgical resection of the tumor resulted in a significant reduction in all the sCD44 proteins, whereas if a surgical resection was not performed the concentrations of the sCD44v5 and sCD44v6 were not reduced prior to surgery. The serum sCD44v6 levels correlated with the venous or lymphatic invasion of the tumor and lymph node metastasis. In addition, a high preoperative serum sCD44v6 level was significantly associated with poor prognosis in patients with gastric cancer. CONCLUSION: The preoperative serum level of sCD44v6 in patients with gastric cancer was significantly higher than that in the healthy controls, and correlated with the venous or lymphatic invasion of the tumor and lymph node metastasis. In addition, a high preoperative serum sCD44v6 level was significantly associated with poor prognosis in patients with gastric cancer. These results suggest that an elevation of the serum sCD44v6 level might be used as a new predictor of tumor invasiveness, and poor prognosis, in patients with gastric cancer.
Alternative Splicing ; Enzyme-Linked Immunosorbent Assay ; Humans ; Lymph Nodes ; Neoplasm Metastasis ; Prognosis ; Stomach Neoplasms*

High Mobility Group I(HMG-I) proteins are nuclear proteins that are required for induction of the human IFN-beta gene by virus and for the regulation of the tumor necrosis-beta factor and rRNA genes. Proteins I and Y result from alternative splicing of a single functional gene named HMGI(Y). In several studies, elevated expressions of the HMGI proteins (HMGI, HMGY, and HMGI-C) have been used as markers in thyroid cancer, but not in adenomas, goiters, and normal thyroid tissues and cells. Here, we try to demonstrate the elevated expression of the HMGI(Y) proteins in thyroid carcinomas by using semi-quantified RT-PCR (Reverse Transcription and Polymerase Chain Reaction). In cases of thyroid carcinomas 4 of 5(80%) were positive, in 10 cases of adenomas, goiters, and normal thyroid tissues, 1(10%) was positive. These results suggest that the semi-quantified RT-PCR is useful preoperative diagnostic tool for differentiating thyroid tumors.
Adenoma ; Alternative Splicing ; Genes, rRNA ; Goiter ; HMGA1a Protein ; Humans ; Nuclear Proteins ; Thyroid Gland* ; Thyroid Neoplasms*

PURPOSE: CD44 is a multifunctional adhesion molecule in cell-to-cell and cell-to-matrix interactions. This transmembrane glycoprotein exists in either standard or variant form, with the variation originating in alternative splicing. This study was designed to evaluate the role of CD44v6, one of the CD44 isoforms, in hepatocellular carcinoma and cholangiocarcinoma. MATERIALS AND METGODS: Immunohistochemical expression of CD44v6 was studied in 7 normal livers, 14 hepatocellular carcinomas and 16 cholangiocarcinomas, that were formalin fixed and paraffin embedded. RESULTS: CD44v6 was frequently expressed in the normal hepatocytes and hepatocellular carcinomas. Expression was not noted in the normal bile duct within the portal tract. CD44v6 was positively expressed in some of the proliferating bile ducts (43%) and cholangiocarcinomas (69%). CONCLUSION: CD44v6 expression may be more important in the stepwise carcinogenesis of the bile duct than in the normal hepatocyte, but further study is needed.
Alternative Splicing ; Bile Ducts ; Carcinogenesis ; Carcinoma, Hepatocellular* ; Cholangiocarcinoma* ; Formaldehyde ; Glycoproteins ; Hepatocytes ; Liver ; Paraffin ; Protein Isoforms

Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.
Alternative Splicing ; Cell Line ; Exons* ; Humans ; Least-Squares Analysis ; Protein Isoforms ; RNA Precursors ; RNA, Messenger ; Transcriptome