Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape

The firmness of table grape berries is a crucial quality parameter. Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive. To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes(DEGs) by comparing the transcriptomes of folic acid(FA)-treated and water-treated(CK) berries at different time points. We then analyzed the sequences to detect alternatively spliced(AS) genes associated with postharvest softening. A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group. There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively. Gene Ontology(GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes,particularly cell wall degradation processes. Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2(VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event. The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries.Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries.

2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-Glucoside modulates CHEK2 and CCND1 alternative splicing to inhibit MCF-7 cells proliferation

Background:In our previous study,we observed a synergistic effect of 2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-glucoside combined with adriamycin to induce apoptosis in MCF-7 breast cancer cells.However,the underlying mechanisms of epigenetic modifications,such as alternative splicing,have not been explored.In this study,we aimed to investigate the mechanism by which THSG inhibits MCF-7 cell proliferation using full-length transcriptome sequencing.Methods:First,cell viability was examined using the methyl thiazolyl tetrazolium method and full-length transcriptome sequencing was performed to identify genes and pathways.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to identify the principal pathways and targets of THSG.Flow cytometry analysis of cell cycle distribution was performed.Meanwhile,the analysis of alternative splicing and domains of the key proteins was conducted.Quantitative polymerase chain reaction and western blotting were performed for verification.Results:THSG showed significant cytotoxic activity in MCF-7 cells.Full-length transcriptome sequencing revealed differential alternative splicing with 173 upregulated and 263 downregulated genes.Further analysis identified distinct differential expression of genes(CHEK2-211 and CCND1-201)involved in the cell cycle in the THSG-treated group.Subsequently,alternative splicing types of CHEK2(mutually exclusive exon)and CCND1(intron retention).We found that THSG downregulated mRNA expression,as confirmed by quantitative polymerase chain reaction analysis.Interestingly,protein structural analysis revealed that THSG treatment led to the generation of CHK2-211,which was the result of a mutation in the amino acid residues(GLU-150,ASN-151)of the CHEK2 domain(VAL-150,GLY-151).and CyclinD1-201 were obtained when an amino acid(ASP-267)in the domain was lost in CyclinD1.Moreover,molecular docking analysis demonstrated that the domains of key proteins could bind THSG more effectively,with no difference in affinity.Western blotting confirmed that THSG inhibited the expression of CHK2 and CyclinD1.Conclusion:THSG modulated the alternative splicing of CHEK2 and CCND1 by inducing G0/G1 cell cycle arrest,consequently suppressing MCF-7 cell proliferation.

Molecular targets and mechanisms of different aberrant alternative splicing in metastatic liver cancer

Metastasis remains a major challenge in the successful management of malignant diseases.The liver is a major site of metastatic disease and a leading cause of death from gastrointestinal malignancies such as colon,stomach,and pancreatic cancers,as well as melanoma,breast cancer,and sarcoma.As an important factor that influences the development of metastatic liver cancer,alternative splicing drives the diversity of RNA transcripts and protein subtypes,which may provide potential to broaden the target space.In particular,the dysfunction of splicing factors and abnormal expression of splicing variants are associated with the occurrence,progression,aggressiveness,and drug resistance of cancers caused by the selective splicing of specific genes.This review is the first to provide a detailed summary of the normal splicing process and alterations that occur during metastatic liver cancer.It will cover the role of alternative splicing in the mechanisms of metastatic liver cancer by examining splicing factor changes,abnormal splicing,and the contribution of hypoxia to these changes during metastasis.

Comprehensive analysis of the full-length transcripts and alternative splicing involved in clubroot resistance in Chinese cabbage

Chinese cabbage is an economically important Brassica vegetable worldwide, and clubroot, which is caused by the soilborne protist plant pathogen Plasmodiophora brassicae is regarded as a destructive disease to Brassica crops. Previous studies on the gene transcripts related to Chinese cabbage resistance to clubroot mainly employed RNA-seq technology,although it cannot provide accurate transcript assembly and structural information. In this study, PacBio RS II SMRT sequencing was used to generate full-length transcriptomes of mixed roots at 0, 2, 5, 8, 13, and 22 days after P. brassicae infection in the clubroot-resistant line DH40R. Overall, 39 376 high-quality isoforms and 26 270 open reading frames(ORFs) were identified from the SMRT sequencing data. Additionally, 426 annotated long noncoding RNAs(lncRNAs),56 transcription factor(TF) families, 1 883 genes with poly(A) sites and 1 691 alternative splicing(AS) events were identified. Furthermore, 1 201 of the genes had at least one AS event in DH40R. A comparison with RNA-seq data revealed six differentially expressed AS genes(one for disease resistance and five for defensive response) that are potentially involved in P. brassicae resistance. The results of this study provide valuable resources for basic research on clubroot resistance in Chinese cabbage.

Alterations of Alternative Splicing Patterns of Ser/Arg-Rich (SR) Genes in Response to Hormones and Stresses Treatments in Different Ecotypes of Rice (Oryza sativa)

Ser/Arg-rich （SR） genes encode proteins that play pivotal roles in both constitutive and alternative splicing of pre-mRNA. However, not much effort has been made to investigate the alternative splicing of their own pre-mRNA. In this study, we conducted comprehensive analyses of pre-mRNA splicing for 22 SR genes in three rice （Oryza sativa L.） ecotypes indica, japonica andjavanica. Using different ecotypes we characterized the variations in expression and splicing patterns of rice SR genes in different tissues and at different developmental stages. In addition, we compared the divergence in expression and splicing patterns of SR genes from seedlings of different rice ecotypes in response to hormones application and environmental stresses. Our results revealed the complexity of alternative splicing of SR genes in rice. The splicing varies in different tissues, in different ecotypes, in response to stresses and hormones. Thus, our study suggested that SR genes were subjected to sophisticated alternative splicing although their encoding proteins were involved in the splicing process.

Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids

Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.

Alternative splicing of VEGFA,APP and NUMB genes in colorectal cancer

AIM:To investigate alternative splicing in vascular endothelial growth factor A(VEGFA),amyloid beta precursor protein(APP),and Numb homolog(NUMB) in colorectal cancer(CRC).METHODS:Real-time quantitative reverse transcriptase polymerase chain reaction(q RT-PCR) and PCRrestriction fragment length polymorphism analyses were performed to detect the expression of VEGFA,APP,and NUMB mR NA in 20 CRC tissues and matched adjacent normal tissues,as well as their alternative splicing variants.RESULTS:q RT-PCR analysis revealed that the expression of APP,NUMB,and VEGFA 165 b m RNA were significantly downregulated,while VEGFA m RNA was upregulated,in CRC tissues(all P < 0.05).PCRrestriction fragment length polymorphism analysis revealed that the expression of VEGFA 165a/b in CRC tissues was significantly higher than in adjacent normal tissues(P < 0.05).Compared with adjacent normal tissues,the expression of NUMB-PRRS in CRC tissues was significantly decreased(P < 0.05),and the expression of NUMB-PRRL was increased(P < 0.05).CONCLUSION:Alternative splicing of VEGFA,APP,and NUMB may regulate the development of CRC,and represent new targets for its diagnosis,prognosis,and treatment.

Modulators of alternative splicing as novel therapeutics in cancer

Alternative splicing(AS), the process of removing introns from pre-m RNA and re-arrangement of exons to give several types of mature transcripts, has been described more than 40 years ago. However, until recently, it has not been clear how extensive it is. Genome-wide studies have now conclusively shown that more than 90% of genes are alternatively spliced in humans. This makes AS one of the main drivers of proteomic diversity and, consequently, determinant of cellular function repertoire. Unsurprisingly, given its extent, numerous splice isoforms have been described to be associated with several dise-ases including cancer. Many of them have antagonistic functions, e.g., pro- and anti-angiogenic or pro- and anti-apoptotic. Additionally several splice factors have been recently described to have oncogene or tumour suppressors activities, like SF3B1 which is frequently mutated in myelodysplastic syndromes. Beside the implications for cancer pathogenesis, de-regulated AS is recognized as one of the novel areas of cell biology where therapeutic manipulations may be designed. This editorial discusses the possibilities of manipulation of AS for therapeutic benefit in cancer. Approaches involving the use of oligonucleotides as well as small molecule splicing modulators are presented as well as thoughts on how specificity might be accomplished in splicing therapeutics.

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

抄写和 post-transcriptional 过程例如其他的拼接，在在 metazoans 控制发展节目起关键作用。最近出现的 RNA-seq 方法把我们真核细胞的 transcriptomes 的理解带到新水平，因为它能两个都同时解决基因表示水平和其他的拼接事件。在性腺获得细胞的区别的更好的理解，我们用 RNA-seq 从果蝇睾丸和卵巢分析了 mRNA 侧面。我们识别了有性特定的 isoforms 在的一套基因野类型(WT ) 性腺，包括几个抄写因素。我们发现从无差别的细菌房间的精子的区别导致了拼接的 RNA 的戏剧的 downregulation 因素。我们的数据证实 RNA 拼接事件是显著地在云石(欺骗) 的无差别的充实房间的袋子里更经常在在 WT 的区别之上的变异的睾丸，而是 downregulated 睾丸。与这一致，我们证明基因在 WT 为成熟分裂和终端区别要求睾丸主要在 transcriptional 水平被调整，然而并非由选择拼接。出人意料地，我们在在无差别的充实房间的欺骗睾丸改变因素和 histone 修改酶的染色质的所有家庭的表示观察了增加。更有趣地，有相反的酶的活动的染色质管理者和 histone 修改酶是在在睾丸的无差别的房间的 coenriched，建议这些房间可以拥有动态染色质建筑学。最后，我们的数据表明果蝇 gonadal transcriptomes 的许多新特征，和愿望导致的更全面的理解微分基因表示并且拼接在果蝇调整 gametogenesis。我们的数据为在果蝇在细菌房间生物学的许多有趣的区域拼接的基因表示和选择的系统的学习提供了一个基础，例如性同种二形和在 germline 干细胞系的增长对终端区别程序的规定的分子的基础。为未加工、分析的 RNA-seq 数据的 GEO 就职数字是 GSE16960。

Alternative splicing: An important mechanism in stem cell biology

Alternative splicing(AS) is an essential mechanism in post-transcriptional regulation and leads to protein diversity. It has been shown that AS is prevalent in metazoan genomes, and the splicing pattern is dynamically regulated in different tissues and cell types, including embryonic stem cells. These observations suggest that AS may play critical roles in stem cell biology. Since embryonic stem cells and induced pluripotent stem cells have the ability to give rise to alltypes of cells and tissues, they hold the promise of future cell-based therapy. Many efforts have been devoted to understanding the mechanisms underlying stem cell selfrenewal and differentiation. However, most of the studies focused on the expression of a core set of transcription factors and regulatory RNAs. The role of AS in stem cell differentiation was not clear. Recent advances in highthroughput technologies have all owed the profiling of dynamic splicing patterns and cis-motifs that are responsible for AS at a genome-wide scale, and provided novel insights in a number of studies. In this review, we discuss some recent findings involving AS and stem cells. An emerging picture from these findings is that AS is integrated in the transcriptional and post-transcriptional networks and together they control pluripotency maintenance and differentiation of stem cells.

Alternative splicing of DNA damage response genes and gastrointestinal cancers

Alternative splicing,which is a common phenomenon in mammalian genomes,is a fundamental process of gene regulation and contributes to great protein diversity.Alternative splicing events not only occur in the normal gene regulation process but are also closely related to certain diseases including cancer.In this review,we briefly demonstrate the concept of alternative splicing and DNA damage and describe the association of alternative splicing and cancer pathogenesis,focusing on the potential relationship of alternative splicing,DNA damage,and gastrointestinal cancers.We will also discuss whether alternative splicing leads to genetic instability,which is considered to be a driving force for tumorigenesis.Better understanding of the role and mechanism of alternative splicing in tumorigenesis may provide new directions for future cancer studies.

DNA methylation and alternative splicing modulate FBXW11 gene expression in Holstein bull testis and are correlated with sperm quality

F-box and WD-40 domain protein 11(FBXW11)is an important component of the E3 ubiquitin-ligase enzyme that plays a key role in the ubiquitin-dependent regulation of spermatogenesis.In our previous research,the mRNA expression of FBXW11 in bull sperm with high motility is significantly higher than that with low motility.In the present study,the protein expression levels of FBXW11 in bull testicular tissues with low-performance sperm quality groups were significantly higher than those in normal performance groups.The immunohistochemistry result demonstrated that FBXW11 protein was located in the periphery of Leydig cells and seminiferous tubules.Three splice variants of the FBXW11 gene,namely,FBXW11-tv1,FBXW11-tv2,and FBXW11-tv3,were identified in testicular tissues.The splicing patterns of the three variants are exon skipping.The transcript FBXW11-tv2 expressions were the highest in each sample.The low-performance groups displayed higher FBXW11-tv1 and FBXW11-tv2 transcript expressions than the normal performance groups.Two CpG islands were located within the 5’UTR and exon 1-2 region of the FBXW11 gene.Bisulfite sequencing PCR results demonstrated that the methylation levels of 11 methylation sites in the CpG island 2 from−99 to−43 in the normal performance groups were significantly lower than those in the low-performance groups.Pearson correlation analysis suggested that the CpG island 2 methylation level was negatively correlated with sperm motility and the transcript FBXW11-tv2 expression level.Our data revealed that alternative splicing and DNA methylation jointly regulated FBXW11 gene expression and were correlated with sperm quality traits during spermatogenesis in Holsteins.

Effects of SNPs and alternative splicing within HGF gene on its expression patterns in Qinchuan cattle

Background： Identification of genetic variants, including SNPs（Single Nucleotide Polymorphisms）, CNVs（Copy Number Variations） and alternative splicing, within functional genes has received increasing attention in animal science research. HGF（Hepatocyte Growth Factor） is a very important growth factor that works as a mitogen or a morphogen during tissue growth, development and regeneration. However, to date, the functions of genetic variants within the bovine HGF gene, particularly their effects on m RNA expression, have not been determined well.Results： The present study aimed to perform association analysis between genetic variants and m RNA expression for the bovine HGF gene in Qinchuan cattle using various strategies, including PCR-RFLP（Restriction Fragment Length Polymorphism）, q PCR（Quantitative Real-time quantitative PCR）, TA cloning, DNA sequencing and bioinformatics analysis. A total of five SNPs were identified and only SV1 locus significantly affected HGF m RNA expression in fetal skeletal muscle（P 〈 0.05）. Heterozygous genotype individuals showed significantly higher HGF expression（P 〈 0.05）, which was significantly greater in the ＂CTCCAGGGTT＂ combined genotype than that in the＂CCCCGGGGTT＂ combined genotype（P 〈 0.05）. In addition, two alternative splicing variations, HGF-W and HGF-M,were identified, which resulted from alternative 3′ splice sites of exon 5, and HGF-W showed higher m RNA levels than HGF-M in all tissues.Conclusion： In summary, genetic variations within the HGF gene affected m RNA expression. These findings provide new insight into the molecular characteristics and functions of bovine HGF.

Regulation of alternative splicing of Bcl-x by IL-6,GM-CSF and TPA

The splicing of many alternative exons in the precursor messenger RNA (pre-mRNA) is regulated by extracellular factors but the underlying molecular bases remain unclear. Here we report the differential regulation of Bcl-x pre-mRNA splicing by extracellular factors and their distinct requirements for pre-mRNA elements. In K562 leukemia cells, treatment with interleukin-6 (IL-6) or granulocyte-macrophage colony stimulating factor (GM-CSF) reduced the proportion of the Bcl-xL variant mRNA while treatment with 12-O-tetradecanoylphorbol 13-acetate (TPA) had no effect. In U251 glioma cells, however, TPA efficiently increased the Bcl-xL level. These regulations were also seen for a transfected splicing reporter mini-gene. Further analyses of deletion mutants indicate that nucleotides 1-176 of the downstream intron are required for the IL-6 effect, whereas additional nucleotides 177-284 are essential for the GM-CSF effect. As for the TPA effect, only nucleotides 1-76 are required in the downstream intron. Thus, IL-6, GM-CSF and TPA differentially regulate Bcl-x splicing and require specific intronic pre-mRNA sequences for their respective effects.

Modification of Alternative Splicing of Bcl-x Pre-mRNA in Bladder Cancer Cells

To modify the splicing pattern of Bcl-x and compare the effect of this approach with that of the antisense gene therapy in BIU-87 cell line of bladder cancer, by using 5′-Bcl-x AS to target downstream alternative 5′-Bcl-x splice site to shift splicing from Bcl-xL to Bcl-xS and 3′-Bcl-x AS antisense to the 3′-splice site of exon Ⅲ in Bcl-x pre-mRNA to down regulation of Bcl-xL expression, the inhibitory effects on cancer cells by modification of alternative splicing and antisense gene therapy were observed and compared by microscopy, MTT Assay, RT-PCR, FACS, Westhern bloting and clone formation. The growth of cells BIU-87 was inhibited in a dose- and time-dependent man- ner. Its inhibitory effect began 12 h after the exposure, reaching a maximum value after 72h. The number of cells decreased in S phase and the number increased in G1 phase. The ability to form loci was reduced and the antisense gene therapy was approximately half as efficient as modification of alternative splicing in inducing apoptosis. It is concluded that modification of splicing pattern of Bcl-x pre-mRNA in bladder cancer cell BIU-87 is better than antisense gene therapy in terms of tumor inhibition.

Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole(Cynoglossus semilaevis)

Chinese tongue sole(Cynoglossus semilaevis)is an economically important marine fish species with a ZZ/ZW sex determination mechanism,which can be influenced by temperature.Alternative splicing(AS)is an important mechanism regulating the expression of genes related to sex determination and gonadal differentiation,but has rarely been reported in fish.In this study,to explore the molecular regulatory mechanisms of sex determination and gonadal differentiation,we combined isoform and RNA sequencing(Iso-Seq and RNA-Seq)to perform transcriptome profiling of male and female gonads in C.semilaevis.In total,81883 and 32341 full-length transcripts were obtained in males and females,respectively.A total of 8279 AS genes were identified,including 2639 genes showing differential AS(DAS)between males and females.Many intersecting DAS genes and differentially expressed genes(DEGs)were enriched in the meiotic cell cycle pathway,and genes related to gonadal differentiation,such as esrrb and wt1a,were found to have sex-specific isoforms.Thus,this study revealed AS events in the gonadal transcriptomes of male and female C.semilaevis,described the characteristics of active transcription in the testes,and identified candidate genes for studying the regulatory mechanisms of AS during gonadal differentiation.

Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis

Heterosis is a well-known phenomenon widely applied in agriculture.Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis.Alternative splicing(AS)is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in plants.However,genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively investigated.We report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and CL11.Our results revealed a large number of significant differential AS(DAS)events in ZD808 relative to its parents,which can be further classified into parental-dominant and novel DAS patterns.Parental-dominant,especially NG5-dominant,events were prevalent in the hybrid,accounting for 42%of all analyzed DAS events.Functional enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis.Among ZD808,CL11,and NG5,32.5%of DAS contained or lacked binding sites of at least one annotated maize microRNA(miRNA)and may be involved in miRNA-mediated posttranscriptional regulation.Cis regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear development.This study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.

Temporal regulation of alternative splicing events in rice memory under drought stress

Plant adaptation to drought stress is essential for plant survival and crop yield.Recently,harnessing drought memory,which is induced by repeated stress and recovery cycles,was suggested as a means to improve drought resistance at the transcriptional level.However,the genetic mechanism underlying drought memory is unclear.Here,we carried out a quantitative analysis of alternative splicing(AS)events in rice memory under drought stress,generating 12 transcriptome datasets.Notably,we identified exon skipping(ES)as the predominant AS type(>80%)in differential alternative splicing(DAS)in response to drought stress.Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94%to 60.70%depending on the species,suggesting that the relative frequency of DAS types in plants is likely to be speciesspecific.The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC.Since U12-type splicing uses the AFAC site,this suggests that drought stress may increase U12-type splicing,and thus increase ES frequency.We hypothesize that multiple isofbrms derived from exon skipping may be induced by drought stress in rice.We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.

Alternative Splicing of OsRAD1 Defines C-Terminal Domain Essential for Protein Function in Meiosis

Alternative splicing can generate multiple mRNAs that differ in their untranslated regions or coding sequences,and these differences might affect mRNA stability or result in different protein isoforms with diverse functions and/or localizations.In this study,we isolated a sterile mutant in rice with abnormal meiosis of microspore mother cells and megaspore mother cells that carried a point mutation in OsRAD1 gene.Cloning of OsRAD1 cDNAs revealed three transcript variants,named as OsRAD1.1,OsRAD1.2 and OsRAD1.3,respectively,which were derived from alternative splicing of the last intron.Proteins derived from the three transcripts were mostly identical except the difference in the very C-terminal domain.The three transcripts exhibited similar expression patterns in various tissues,but the expression level of OsRAD1.1 was the highest.Specific knockout of OsRAD1.1 led to sterility,while knockout of OsRAD1.2 and OsRAD1.3 together did not change the plant fertility.Overexpression of OsRAD1.2 and OsRAD1.3 cDNAs in OsRAD1.1-specific mutant did not complement the plant fertility.Yeast two-hybrid assay showed that OsRAD1.1,but not OsRAD1.2 and OsRAD1.3,interacted with the three other meiosis proteins OsHUS1,OsRAD9 and OsRAD17,suggesting that the C-terminal domain of OsRAD1.1 is critical for the protein function.

Alternative RNA splicing in stem cells and cancer stem cells:Importance of transcript-based expression analysis

Alternative ribonucleic acid(RNA)splicing can lead to the assembly of different protein isoforms with distinctive functions.The outcome of alternative splicing(AS)can result in a complete loss of function or the acquisition of new functions.There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells(CSCs),and their prospective contribution in cancer progression.AS directly regulates the self-renewal features of stem cells(SCs)and stem-like cancer cells.Notably,octamer-binding transcription factor 4A spliced variant of octamerbinding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs.The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness.The alternative spliced variants of CSCs markers,including cluster of differentiation 44,aldehyde dehydrogenase,and doublecortin-like kinase,α6β1 integrin,have pivotal roles in increasing selfrenewal properties and maintaining the pluripotency of CSCs.Various splicing analysis tools are considered in this study.LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events.Additionally,LeafCutter can be used for efficient mapping splicing quantitative trait loci.Altogether,the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.