scholarly journals Multi-level regulation of PKCδI alternative splicing by lithium chloride

2020 ◽  
Author(s):  
Deena Bader ◽  
Rekha S. Patel ◽  
Ashley Lui ◽  
Chetna Thawani ◽  
Rea Rupani ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Lithium Chloride ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Fine Tuning ◽  
Serine Threonine Kinase ◽  
Rna Immunoprecipitation ◽  
Alternatively Spliced ◽  
Licl Treatment ◽  
Lncrna Neat1

Lithium chloride (LiCl) is commonly used in treatment of mood disorders, however its usage leads to weight gain which promotes metabolic disorders. Protein Kinase C delta (PKCδ), a serine/threonine kinase, is alternatively spliced to PKCδI and PKCδII in 3T3L1 cells. We previously demonstrated that PKCδI is the predominantly expressed isoform in 3T3L1 pre-adipocytes. Here, we demonstrate that LiCl treatment decreases PKCδI levels, increases formation of lipid droplets and increases oxidative stress. Hence, we investigated the molecular mechanisms underlying the regulation of PKCδI alternative splicing by LiCl. We previously demonstrated that the splice factor SFRS10 is essential for PKCδI splicing. Our results demonstrate that GSK3ß phosphorylates SFRS10 and SFRS10 is in a complex with long noncoding RNA NEAT1 to promote PKCδI splicing. Using PKCδ splicing minigene and RNA-immunoprecipitation assays, our results demonstrate that upon LiCl treatment, NEAT1 levels are reduced, GSK3ß activity is inhibited and SFRS10 phosphorylation is decreased which leads to decreased expression of PKCδI. Integration of the GSK3ß signaling pathway with the ribonucleoprotein complex of lncRNA NEAT1 and SFRS10 enables fine tuning of PKCδI expression during adipogenesis. Knowledge of the molecular pathways impacted by LiCl provide an understanding of the ascent of obesity as a comorbidity in disease management.

scholarly journals LncRNA NEAT1 Promotes High Glucose-Induced Mesangial Cell Hypertrophy by Targeting miR-222-3p/CDKN1B Axis

2021 ◽  
Vol 7 ◽  
Author(s):  
Lin Liao ◽  
Jie Chen ◽  
Chuanfu Zhang ◽  
Yue Guo ◽  
Weiwei Liu ◽  
...  
Keyword(s):  
High Glucose ◽  
Noncoding Rna ◽  
Mesangial Cell ◽  
Mesangial Cells ◽  
Morphological Alteration ◽  
Glomerular Hypertrophy ◽  
Cell Hypertrophy ◽  
Rna Immunoprecipitation ◽  
Lncrna Neat1

Glomerular hypertrophy is an early morphological alteration in diabetic nephropathy. Cyclin-Dependent Kinases have been shown to be required for high glucose (HG)-induced hypertrophy; however, the upstream regulators of CDKN1B in glomerular hypertrophy remain unclear. Herein we describe a novel pathway in which Long noncoding RNA (lncRNA) NEAT1 regulates the progression of mesangial cell hypertrophy via a competing endogenous RNA (ceRNA) mechanism. Real-time PCR was performed to detect the relative NEAT1 and miR-222-3p expressions and further confirmed the relationship between NEAT1 and miR-222-3p. Cell cycle was evaluated by flow cytometry. The related mechanisms were explored by Western blot, RNA immunoprecipitation and chromatin immunoprecipitation assay. We show that NEAT1 forms double stranded RNA (dsRNA) with miR-222-3p, thus limiting miR-222-3p’s binding with CDKN1B. This release of CDKN1B mRNA leads to elevated CDKN1B protein expression, resulting in hypertrophy. In addition, we demonstrated that STAT3 which is activated by HG induces the transcription of NEAT1 by binding to its promoter. Our findings underscore an unexpected role of lncRNAs on gene regulation and introduce a new mode of proliferation regulation in mesangial cells.

scholarly journals LncRNA DANCR functions as a competing endogenous RNA to regulate RAB1A expression by sponging miR-634 in glioma

2018 ◽  
Vol 38 (1) ◽  
Author(s):  
Dawei Xu ◽  
Jian Yu ◽  
Guojun Gao ◽  
Guangjian Lu ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Cell Lines ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Glioma Cells ◽  
Tumor Grade ◽  
Underlying Mechanism ◽  
Luciferase Reporter ◽  
Biological Functions ◽  
Advanced Tumor ◽  
Rna Immunoprecipitation

Long noncoding RNA (lncRNA) differentiation antagonizing nonprotein coding RNA (DANCR) plays important regulatory roles in many solid tumors. However, the effect of DANCR in glioma progression and underlying molecular mechanisms were not entirely explored. In the present study, we determined the expression of DANCR in glioma tissues and cell lines using qRT-PCR and further defined the biological functions. Furthermore, we used luciferase reporter assay, Western blot, and RNA immunoprecipitation (RIP) to explore the underlying mechanism. Our results showed that DANCR was significantly up-regulated in glioma tissues and cell lines (U251, U118, LN229, and U87MG). High DANCR expression was correlated with advanced tumor grade. Inhibition of DANCR suppressed the glioma cells proliferation and induced cells arrested in the G0/G1 phase. In addition, we verified that DANCR could directly interact with miR-634 in glioma cells and this interaction resulted in the inhibition of downstream of RAB1A expression. The present study demonstrated that DANCR/miR-634/RAB1A axis plays crucial roles in the progression of glioma, and DANCR might potentially serve as a therapeutic target for the treatment of glioma patients.

scholarly journals An Arabidopsis long noncoding RNA modulates the transcriptome through interactions with a network of splicing factors

2020 ◽  
Author(s):  
Richard Rigo ◽  
Jérémie Bazin ◽  
Natali Romero-Barrios ◽  
Michaël Moison ◽  
Leandro Lucero ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Root Formation ◽  
Noncoding Rnas ◽  
Dynamic Network ◽  
Splicing Factors ◽  
Genome Wide ◽  
A Minor ◽  
Conserved Core

ABSTRACTAlternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyzed the effect of the knockdown and overexpression of ASCO at genome-wide level and found a high number of deregulated and differentially spliced genes, related to flagellin responses and biotic stress. In agreement, roots from ASCO-knocked down plants are more sensitive to flagellin. Surprisingly, only a minor subset of genes overlapped with the AS defects of the nsra/b double mutant. Using biotin-labelled oligonucleotides for RNA-mediated ribonucleoprotein purification, we found that ASCO binds to the highly conserved core spliceosome component PRP8a. ASCO deregulation impairs the recognition of specific flagellin-related transcripts by PRP8a and SmD1b, another spliceosome component, suggesting that ASCO function regulates AS through the interaction with multiple splicing factors. Hence, lncRNAs may interact in a dynamic network with many splicing factors to modulate transcriptome reprogramming in eukaryotes.

scholarly journals Epigenetic Regulation of Gibberellin Metabolism and Signaling

2020 ◽  
Vol 61 (11) ◽  
pp. 1912-1918 ◽  
Author(s):  
Yongyao Xie ◽  
Letian Chen
Keyword(s):  
Chromatin Remodeling ◽  
Epigenetic Regulation ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Fine Tuning ◽  
Regulatory Mechanisms ◽  
Gibberellin Metabolism ◽  
Important Means ◽  
Environmental Responses ◽  
Insight Into

Abstract The precise regulation of gibberellin (GA) metabolism and signaling is essential for plant development and environmental responses. Epigenetic regulatory mechanisms, such as histone modification, noncoding RNA-mediated regulation, chromatin remodeling and DNA methylation, are emerging as important means of fine-tuning gene expression. Recent studies have significantly improved our understanding of the relationships between epigenetic regulation and GA metabolism and signaling. Here, we summarize the molecular mechanisms by which epigenetic modifications affect GA metabolism and signaling pathways and provide new insight into an unfolding avenue of research related to the epigenetic regulation of GA pathways.

scholarly journals circAkap17b acts as a miR-7 family molecular sponge to regulate FSH secretion in rat pituitary cells

2020 ◽  
Vol 65 (4) ◽  
pp. 135-148
Author(s):  
Chang-Jiang Wang ◽  
Fei Gao ◽  
Yi-Jie Huang ◽  
Dong-Xu Han ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Pituitary Cells ◽  
Rat Pituitary ◽  
Rna Immunoprecipitation ◽  
Rat Pituitary Cells

The pituitary gland functions as a prominent regulator of diverse physiologic processes by secreting multiple hormones. Circular RNAs (circRNAs) are an emerging novel type of endogenous noncoding RNA that have recently been recognized as powerful regulators participating in various biological processes. However, the physiological roles and molecular mechanisms of circRNAs in pituitary remain largely unclear. Herein, we concentrated on expounding the biological function and molecular mechanism of circRNA in rat pituitary. In this study, we identified a novel circRNA in pituitary tissue, circAkap17b, which was pituitary- and stage-specific. Then, we designed circAkap17b siRNA and constructed an overexpression plasmid to evaluate the effect of loss- and gain-of-circAkap17b function on FSH secretion. Interestingly, silencing circAkakp17b significantly inhibited FSH expression and secretion, while overexpression of circAkap17b enhanced FSH expression and secretion. Furthermore, dual luciferase reporter and RNA immunoprecipitation (RIP) assays confirmed that circAkap17b could serve as miR-7 sponge to regulate target genes. Additionally, miR-7b suppressed FSH expression and secretion by directly targeting Fshb through the dual luciferase reporter and RT-qPCR analysis. Additionally, rescue experiments showed that circAkap17b could regulate FSH secretion in pituitary cells through a circAkap17b-miR-7-Fshb axis. Collectively, we demonstrated that circAkap17b could act as a molecular sponge of miR-7 to upregulate expression of the target gene Fshb and facilitate FSH secretion. These findings provide evidence for a novel regulatory role of circRNAs in pituitary.

scholarly journals Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Wang ◽  
Geng G. Tian ◽  
Zhuxia Zheng ◽  
Bo Li ◽  
Qinghe Xing ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Candidate Genes ◽  
Sexual Differentiation ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Gonadal Development ◽  
Transcriptome Database ◽  
Alternatively Spliced ◽  
Expression Module

Abstract Background Mammalian gonadal development is crucial for fertility. Sexual differentiation, meiosis and gametogenesis are critical events in the process of gonadal development. Abnormalities in any of these events may cause infertility. However, owing to the complexity of these developmental events, the underlying molecular mechanisms are not fully understood and require further research. Results In this study, we employed RNA sequencing to examine transcriptome profiles of murine female and male gonads at crucial stages of these developmental events. By bioinformatics analysis, we identified a group of candidate genes that may participate in sexual differentiation, including Erbb3, Erbb4, and Prkg2. One hundred and two and 134 candidate genes that may be important for female and male gonadal development, respectively, were screened by analyzing the global gene expression patterns of developing female and male gonads. Weighted gene co-expression network analysis was performed on developing female gonads, and we identified a gene co-expression module related to meiosis. By alternative splicing analysis, we found that cassette-type exon and alternative start sites were the main forms of alternative splicing in developing gonads. A considerable portion of differentially expressed and alternatively spliced genes were involved in meiosis. Conclusion Taken together, our findings have enriched the gonadal transcriptome database and provided novel candidate genes and avenues to research the molecular mechanisms of sexual differentiation, meiosis, and gametogenesis.

scholarly journals The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 367
Author(s):  
Katherine E. Havranek ◽  
Luke Adam White ◽  
Thomas C. Bisom ◽  
Jean-Marc Lanchy ◽  
J. Stephen Lodmell
Keyword(s):  
Alternative Splicing ◽  
Mammalian Cells ◽  
Rift Valley Fever Virus ◽  
Critical Role ◽  
Fine Tuning ◽  
Interferon Response ◽  
Type I ◽  
Interferon Signaling ◽  
Valley Fever ◽  
Alternatively Spliced

In recent years, transcriptome profiling studies have identified changes in host splicing patterns caused by viral invasion, yet the functional consequences of the vast majority of these splicing events remain uncharacterized. We recently showed that the host splicing landscape changes during Rift Valley fever virus MP-12 strain (RVFV MP-12) infection of mammalian cells. Of particular interest, we observed that the host mRNA for Rio Kinase 3 (RIOK3) was alternatively spliced during infection. This kinase has been shown to be involved in pattern recognition receptor (PRR) signaling mediated by RIG-I like receptors to produce type-I interferon. Here, we characterize RIOK3 as an important component of the interferon signaling pathway during RVFV infection and demonstrate that RIOK3 mRNA expression is skewed shortly after infection to produce alternatively spliced variants that encode premature termination codons. This splicing event plays a critical role in regulation of the antiviral response. Interestingly, infection with other RNA viruses and transfection with nucleic acid-based RIG-I agonists also stimulated RIOK3 alternative splicing. Finally, we show that specifically stimulating alternative splicing of the RIOK3 transcript using a morpholino oligonucleotide reduced interferon expression. Collectively, these results indicate that RIOK3 is an important component of the mammalian interferon signaling cascade and its splicing is a potent regulatory mechanism capable of fine-tuning the host interferon response.

scholarly journals Long noncoding RNA TUG1 promotes proliferation and inhibits apoptosis in multiple myeloma by inhibiting miR-29b-3p

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Dahai Liu ◽  
Jianfeng Wang ◽  
Meihan Liu
Keyword(s):  
Multiple Myeloma ◽  
Cell Lines ◽  
Histone Deacetylases ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Cell Counting ◽  
Luciferase Reporter ◽  
Expression Levels ◽  
Real Time Quantitative Pcr ◽  
Rna Immunoprecipitation

Abstract Background: Long non-coding RNA taurine up-regulated gene 1 (TUG1) was reportedly involved in initiation and development of several cancers. However, its function and molecular mechanisms in multiple myeloma (MM) are still unclear. The present study aimed to determine the expression status, biological function, and potential mechanisms of TUG1 in the progression of MM. Materials and methods: The expression levels of TUG1 were examined in MM samples and cell lines by real-time quantitative PCR. The effects of TUG1 on MM cells proliferation and apoptosis were assessed using Cell Counting Kit-8 assay and flow cytometry respectively. MiRNAs-targeted sites in TUG1 were screened by Starbase2.0 and were identified by RNA immunoprecipitation assay combined with luciferase reporter assay. Results: The expression levels of TUG1 were markedly increased in MM samples and cell lines. Knockdown of TUG1 significantly suppressed the proliferation, induced cell cycle arrest at G1/G0 phase, and promoted apoptosis of MM cells. In exploring the regulatory mechanism, miR-29b-3p was confirmed to be a direct target of TUG1, and repression of miR-29b-3p could partially rescue the effect TUG1 knockdown on MM cell proliferation, cycle, and apoptosis. In addition, TUG1 positively modulated histone deacetylases 4 (HDAC4, a target of miR-29b-3p) expression through sponging of miR-29b-3p in MM cells. Conclusion: These findings suggested that TUG1 exerted an oncogenic role in MM by acting as a competing endogenous RNA of miR-29b-3p, and implied the potential application of TUG1 in treatment for MM.

scholarly journals Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 285
Author(s):  
Saurabh Chaudhary ◽  
Meenu Kalkal
Keyword(s):  
Alternative Splicing ◽  
Fine Tuning ◽  
Differentially Expressed ◽  
Environmental Damage ◽  
Dependent Manner ◽  
Transcriptional Dynamics ◽  
Crop Varieties ◽  
Alternatively Spliced ◽  
Use Efficiency ◽  
N Starvation

Nitrogen (N) is crucial for plant growth and development; however, excessive use of N fertilizers cause many problems including environmental damage, degradation of soil fertility, and high cost to the farmers. Therefore, immediate implementation is required to develop N efficient crop varieties. Rice being low nitrogen use efficiency (NUE) and a high demand staple food across the world has become a favorite crop to study the NUE trait. In the current study, we used the publicly available transcriptome data generated from the root and shoot tissues of two rice genotypes IR-64 and Nagina-22 (N-22) under optimum N supply (N+) and chronic N-starvation (N−). A stringent pipeline was applied to detect differentially expressed genes (DEGs), alternatively spliced (DAS) genes, differentially expressed transcripts (DETs) and differential transcript usage (DTU) transcripts in both the varieties and tissues under N+ and N− conditions. The DAS genes and DTU transcripts identified in the study were found to be involved in several metabolic and biosynthesis processes. We suggest alternative splicing (AS) plays an important role in fine-tuning the regulation of metabolic pathways related genes in genotype, tissue, and condition-dependent manner. The current study will help in understanding the transcriptional dynamics of NUE traits in the future.

scholarly journals Biophysical characterization of melanoma cell phenotype markers during metastatic progression

2021 ◽  
Author(s):  
Anna Sobiepanek ◽  
Alessio Paone ◽  
Francesca Cutruzzolà ◽  
Tomasz Kobiela
Keyword(s):  
Molecular Mechanisms ◽  
Cell Metabolism ◽  
Structural Features ◽  
Protein Glycosylation ◽  
Cell Phenotype ◽  
Metastatic Progression ◽  
Label Free ◽  
Serine Threonine Kinase ◽  
Biophysical Characterization ◽  
Viscoelastic Parameters

AbstractMelanoma is the most fatal form of skin cancer, with increasing prevalence worldwide. The most common melanoma genetic driver is mutation of the proto-oncogene serine/threonine kinase BRAF; thus, the inhibition of its MAP kinase pathway by specific inhibitors is a commonly applied therapy. However, many patients are resistant, or develop resistance to this type of monotherapy, and therefore combined therapies which target other signaling pathways through various molecular mechanisms are required. A possible strategy may involve targeting cellular energy metabolism, which has been recognized as crucial for cancer development and progression and which connects through glycolysis to cell surface glycan biosynthetic pathways. Protein glycosylation is a hallmark of more than 50% of the human proteome and it has been recognized that altered glycosylation occurs during the metastatic progression of melanoma cells which, in turn facilitates their migration. This review provides a description of recent advances in the search for factors able to remodel cell metabolism between glycolysis and oxidative phosphorylation, and of changes in specific markers and in the biophysical properties of cells during melanoma development from a nevus to metastasis. This development is accompanied by changes in the expression of surface glycans, with corresponding changes in ligand-receptor affinity, giving rise to structural features and viscoelastic parameters particularly well suited to study by label-free biophysical methods.

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