Regulation Of Gene Splicing Research Articles

Alternative splicing responses to salt stress in Glycyrrhiza uralensis revealed by global profiling of transcriptome RNA-seq datasets.

Excessive reactive oxygen species stress due to salinity poses a significant threat to the growth of Glycyrrhiza uralensis Fisch. To adapt to salt stress, G. uralensis engages in alternative splicing (AS) to generate a variety of proteins that help it withstand the effects of salt stress. While several studies have investigated the impact of alternative splicing on plants stress responses, the mechanisms by which AS interacts with transcriptional regulation to modulate the salt stress response in G. uralensis remain poorly understood. In this study, we utilized high-throughput RNA sequencing data to perform a comprehensive analysis of AS events at various time points in G. uralensis under salt stress, with exon skipping (SE) being the predominant AS type. KEGG enrichment analysis was performed on the different splicing genes (DSG), and pathways associated with AS were significantly enriched, including RNA transport, mRNA surveillance, and spliceosome. This indicated splicing regulation of genes, resulting in AS events under salt stress conditions. Moreover, plant response to salt stress pathways were also enriched, such as mitogen-activated protein kinase signaling pathway - plant, flavonoid biosynthesis, and oxidative phosphorylation. We focused on four differentially significant genes in the MAPK pathway by AS and qRT-PCR analysis. The alternative splicing type of MPK4 and SnRK2 was skipped exon (SE). ETR2 and RbohD were retained intron (RI) and alternative 5'splice site (A5SS), respectively. The expression levels of isoform1 of these four genes displayed different but significant increases in different tissue sites and salt stress treatment times. These findings suggest that MPK4, SnRK2, ETR2, and RbohD in G. uralensis activate the expression of isoform1, leading to the production of more isoform1 protein and thereby enhancing resistance to salt stress. These findings suggest that salt-responsive AS directly and indirectly governs G. uralensis salt response. Further investigations into AS function and mechanism during abiotic stresses may offer novel references for bolstering plant stress tolerance.

OsGRF4AA compromises heat tolerance of developing pollen grains in rice.

Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA ), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.

Manipulating mRNA splicing by base editing in plants.

Precursor-mRNAs (pre-mRNA) can be processed into one or more mature mRNA isoforms through constitutive or alternative splicing pathways. Constitutive splicing of pre-mRNA plays critical roles in gene expressional regulation, such as intron-mediated enhancement (IME), whereas alternative splicing (AS) dramatically increases the protein diversity and gene functional regulation. However, the unavailability of mutants for individual spliced isoforms in plants has been a major limitation in studying the function of mRNA splicing. Here, we describe an efficient tool for manipulating the splicing of plant genes. Using a Cas9-directed base editor, we converted the 5' splice sites in four Arabidopsis genes from the activated GT form to the inactive AT form. Silencing the AS of HAB1.1 (encoding a type 2C phosphatase) validated its function in abscisic acid signaling, while perturbing the AS of RS31A revealed its functional involvement in plant response to genotoxic treatment for the first time. Lastly, altering the constitutive splicing of Act2 via base editing facilitated the analysis of IME. This strategy provides an efficient tool for investigating the function and regulation of gene splicing in plants and other eukaryotes.

Morphophysiological effects of insertional mutagenesis of the contactin 5 (Cntn5) gene in transgenic mice

The transgenesis technologies are actively used in different fields of biological studies. The most actively used method to obtain transgenic animals by DNA injection in the zygote pronucleus can be accompanied by the violation of the genes’ function instead of integrating the transgenic construction. In this work, the morphophysiological effects of integrating the transgenic construction providing the production of the human granulocyte–macrophage colony-stimulating factor in the milk of the mouse line (GM9) (the insertion of the construction in the intron of the contactin 5 (Cntn5) gene) were described. It was demonstrated that the insertion of the construction did not result in the Cntn5 knockout. However, the gene transcription in the heart and kidneys of transgenic animals changes compared with wild-type animals, and the spectrum of transcripts also changes, indicating a violation in the Cntn5 gene splicing regulation. It is known from the published data that the Cntn5 polymorphisms are associated with an addiction to obesity and a predisposition to arterial hypertension. We studied the main parameters of the fat metabolism and cardiovascular activity in mice homozygous for the transgene insertion in the Cntn5 gene, heterozygous animals, and wild-type animals. The phenotyping carried out demonstrates that homozygous mice have a smaller body weight than wild-type individuals. And the weight difference between genotypes is determined more by significantly lower fat accumulation than by the lag of mutants in the development of the skeleton and muscles constituting the lean mass. Statistically significant differences in the parameters characterizing the intensity of the blood circulation were found in the studied lines. Homozygous mice exceed wild-type individuals by their arterial pressure values, heart rate, and blood flow rate in the tail vessels. It should be noted that heterozygous individuals have intermediate values between mutants and wild-type according to all the measured morphofunctional parameters.

Functional and Clinical Relevance of Splicing Factor SRSF1 in Multiple Myeloma (MM)

The mechanisms modifying expression and function of genes, such as alternative pre-mRNA splicing or microRNA (miRNA) activity, need to be considered in order to provide a more accurate genomic framework for clinical correlation, as well as for high value therapeutic target discovery. Aberrant splicing of numerous genes has been reported in other malignancies, including a small number of genes reported in MM. The emerging focus therefore, has been to understand the molecular mechanisms driving alternate splicing. Several studies provide evidence that an abnormally expressed splicing factor can have oncogenic properties by impacting alternative splicing of cancer-associated genes.Based on our previously described significant role of E2F1 and its heterodimerization partner Dp1 in myeloma, we evaluated their chromatin binding targets related with splicing factors. Using genome wide chromatin and transcription landscape mapping techniques, we observed both transcription factors bound to the promoter of several splicing factors including Serine Arginine-Rich Splicing Factor 1 (SRSF1). Further evaluation in our gene expression profile from 170 newly-diagnosed myeloma patients, identified high expression of SRSF1 in MM compared to normal plasma cells, with a significant difference in the non-hyperdiploid subtype. Importantly, we have observed significant coexpression of Dp1 and SRSF1 in this dataset suggesting a mechanism for SRSF1 upregulation in tumors with elevated Dp1. SRSF1 has been shown to be overexpressed in human tumors with elevated Myc. No correlation between Myc with SRSF1 was observed in myeloma suggesting that SRSF1 expression is mediated by Myc-independent mechanism.We next explored the functional role of SRSF1 in MM. In gain-of-function experiments, enforced expression of SRSF1-eGFP in MM1S significantly increased proliferation. Conversely, downregulation of SRSF1 with specific shRNAs in MM cell lines significantly inhibited MM cell proliferation and cell survival. These data underscore the oncogenic potential of SRSF1 in MM. A significant reduction in SRSF1 at mRNA and protein levels was observed after E2F1 and/or Dp1 gene silencing. Moreover, peptide-based strategy to abrogate interaction between Dp1-E2F1 led to decreased SRSF1 expression levels.Importantly, the increased expression of SRSF1 was linked with overall survival in 2 independent MM datasets, highlighting for the first time the clinical relevance of splicing related factors in myeloma.In conclusion our results indicate a functional role and clinical significance of a gene involved in regulation of gene splicing. This study highlights the need to further understand the splicing pattern in myeloma and also supports the emerging concept that splicing programs, together with transcriptional programs participate in the altered cellular function during tumor initiation and progression. DisclosuresAnderson:Celgene: Consultancy; Sanofi-Aventis: Consultancy; Onyx: Consultancy; Acetylon: Scientific Founder, Scientific Founder Other; Oncoprep: Scientific Founder Other; Gilead Sciences: Consultancy.

GREMET: An integrative tool for the prediction of mutation effects on gene regulation

The identification of thousands of mutations yearly has put new challenges to researchers who are interested in fast and effective annotation as well as the prediction of potential implications to the gene regulation mechanisms. This work presents an integrative tool, called GREMET, for the prediction of alterations in gene splicing regulation inferred by mutations of the human genome. GREMET supports the characterization of mutations either single-point or indels with respect to their effect on the splicing potential of the neighboring sequences and the binding strength of auxiliary cis-acting splicing enhancers. In addition, GREMET identifies possible consequences of mutations on the DNA methylation through the disruption or creation of CpG sequences. Besides locus-specific mutations, GREMET performs the analyses on newly identified mutations and provides an easy-to-use Web interface helping researchers to save time in routine mutation analyses. GREMET is freely accessible at: http://kedip.med.auth.gr/biotools/gremet/.

Haploinsufficiency of RPS14 and RPS24 in 5q-Syndrome

Abstract 4964The 5q-syndrome is a subtype of myelodysplastic syndrome, a rare disorder caused by the loss of a part of the long arm of chromosome 5, being firstly described in 1974 by Van Den Berghe; the cytogenetic characterization reports 4 types of deletion of chromosome 5 (q13-q31), (q13-q33), (q22-q25), (q32-q33) in a critical deletion region (CDR 1 and 2), that shows a reduction in gene expression of 50–60%, the aploinsufficiency includes the tumor suppressor genes, the regulation of gene splicing and apoptosis, the growth inhibitory protein, and the PDGF and p53 pathway. The CDR1 deletion involves genes encoding the 40S ribosomal subunit (D55479-CDC23, EGR1, CDC25C), while the CDR2 deletion includes several genes (SPARC, WIG-1, BMI-1, MEGF-1, RPS14, RPS24) encoding the transcription factor Egr-1/K20×20, the cytoskeletal remodeling protein, and the alphacatenin.The mechanism of the aploinsufficiency remains unresolved, but we have observed the characteristic changes Cys224-with Arg234, and the down-regulation of micro RNA-genes RPL28, EF1D, and up-regulation of several pro-apoptotic genes BAX and CAPS3, that is caused by a defect in ribosomal protein function, which is characterized by macrocytic anemia, thrombocytosis, megakaryocyte hyperplasia with nuclear hypolobation, erythroblastopenia associated with displastic abnormalities of hematopoietic stem cells/progenitor cells (HSCs/HPCs), hypogranular neutrophils or pseudo Chediak-Higashi large granules, ringed sideroblasts, excess of blasts, and increased malignancy (acute myeloid leukemia).In accordance of what recent data are currently suggesting we have also observed the mutation of the JaK2 gene and FLT3; this means that many other candidate genes may play a role in this disease and in the risk for clonal evolution and in the progression of acute myeloid leukemia. Disclosures:No relevant conflicts of interest to declare.

Application of Tobacco Transient Expression System to Detect Gene Splicing in Higher Plants*

To dissect the splicing mechanism is a critical step in understanding the plant morphogenesis, growth, development and responses to stresses. Compared to animals, the research on RNA splicing is progressing poorly in plants. The splicing patterns of gene fragments derived from monocot rice BADH2 and dicot Arabidopsis GR7 were detected by Agrobacterium-mediated tobacco transient expression system. The results indicated that the fundamental splicing regulatory elements are conserved in plants. The tobacco transient expression system could be used as an important tool for fast and sensitive detection of gene splicing regulation in higher plants.

Qualitative and quantitative analysis of the effect of splicing mutations in propionic acidemia underlying non-severe phenotypes.

In this work we analyze splicing mutations identified in propionic acidemia patients to clarify their functional effects and their involvement in the disease phenotype. Two mutations in the PCCA gene detected in homozygous patients and involving consensus splice sequences (IVS21+3del4 and IVS22-2A>G) were shown to produce some normal splicing in patients' cells, at very low levels, which were quantitated by real-time PCR methods, and which presumably are sufficient to moderate the phenotype. We have also analysed the effect of mutations c.653A>G and IVS10-11del6 in the PCCB gene present in heterozygous patients with mild phenotype. The c.653A>G mutation is located in the last codon of exon 6 and interferes with the correct spliceosomal assembly activating a cryptic splice site within exon 6, which leads to an in-frame six-nucleotide deletion (delV217-K218). Minigene analysis and sequence-specific hybridization probes using real-time PCR methods showed that no normally spliced transcript is detectable in the patients' fibroblasts. The IVS10-11del6 mutation shortens the polypyrimidine tract of the 3'-splice site of exon 11, resulting in exon skipping. Some normal transcript is detectable by allele-specific hybridization probes. These analyses suggest that, in some cases, the regulation of gene splicing can potentially play an important role in human disease influencing phenotypic parameters.

Dutch May Legislate Gene–Splicing Regulation

Dutch May Legislate Gene–Splicing Regulation