The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function*

2021 ◽  
Author(s):  
Davia Blake ◽  
Kristen W. Lynch
Keyword(s):  
Alternative Splicing ◽  
Immune Function ◽  
Alternative Polyadenylation

scholarly journals RNA Expression Profile and Alternative Splicing Signatures of Genistein-Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-19
Author(s):  
Zengpeng Lv ◽  
Jingle Jiang ◽  
Chao Ning ◽  
Hongjian Dai ◽  
Song Jin ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Immune Function ◽  
Expression Profiles ◽  
Egg Laying ◽  
High Dose ◽  
Rna Expression ◽  
Broiler Breeder ◽  
Breeder Hens ◽  
Laying Performance ◽  
Hepatic Transcriptome

Little information has been available about the influence of dietary genistein (GEN) on hepatic transcriptome of laying broiler breeder (LBB) hens. The study is aimed at broadening the understanding of RNA expression profiles and alternative splicing (AS) signatures of GEN-treated breeder hens and thereby improving laying performance and immune function of hens during the late egg-laying period. 720 LBB hens were randomly allocated into three groups with supplemental dietary GEN doses (0, 40 mg/kg, and 400 mg/kg). Each treatment has 8 replicates of 30 birds. Dietary GEN enhanced the antioxidative capability of livers, along with the increased activities of glutathione peroxidase and catalase. Furthermore, it improved lipid metabolic status and apoptotic process in the liver of hens. 40 mg/kg dietary GEN had the better effects on improving immune function and laying performance. However, transcriptome data indicated that 400 mg/kg dietary GEN did negative regulation of hormone biosynthetic process. Also, it upregulated the expressions of EDA2R and CYR61 by the Cis regulation of neighbouring genes (lncRNA_XLOC_018890 and XLOC_024242), which might activate NF-κB and immune-related signaling pathway. Furthermore, dietary GEN induced AS events in the liver, which also enriched into immune and metabolic process. Therefore, the application of 40 mg/kg GEN in the diet of breeder hens during the late egg-laying period can improve lipid metabolism and immune function. We need to pay attention to the side-effects of high-dose GEN on the immune function.

scholarly journals Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ning Li ◽  
Ziwei Meng ◽  
Minjie Tao ◽  
Yueyuan Wang ◽  
Yulan Zhang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptome Analysis ◽  
Spinacia Oleracea ◽  
Sex Differentiation ◽  
Alternative Polyadenylation ◽  
Gender Development ◽  
Comparative Transcriptome ◽  
Male And Female ◽  
First Time ◽  
Female Flowers

Abstract Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant.

scholarly journals DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1453 ◽  
Author(s):  
Jamal Elhasnaoui ◽  
Valentina Miano ◽  
Giulio Ferrero ◽  
Elena Doria ◽  
Antonette E. Leon ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Clinical Data ◽  
Noncoding Rna ◽  
Estrogen Receptor Alpha ◽  
Exon Skipping ◽  
Alternative Polyadenylation ◽  
Luminal A ◽  
Her2 Positive ◽  
Public Datasets ◽  
Nuclear Ribonucleoprotein

DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.

scholarly journals Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns (560.2)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Maliheh Movassat ◽  
Tara Crabb ◽  
Anke Busch ◽  
Yongsheng Shi ◽  
Klemens Hertel
Keyword(s):  
Alternative Splicing ◽  
Alternative Polyadenylation

scholarly journals Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

RNA Biology ◽  
2016 ◽  
Vol 13 (7) ◽  
pp. 646-655 ◽  
Author(s):  
Maliheh Movassat ◽  
Tara L. Crabb ◽  
Anke Busch ◽  
Chengguo Yao ◽  
Derrick J. Reynolds ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Alternative Polyadenylation

scholarly journals Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kevin C. H. Ha ◽  
Timothy Sterne-Weiler ◽  
Quaid Morris ◽  
Robert J. Weatheritt ◽  
Benjamin J. Blencowe
Keyword(s):  
Alternative Splicing ◽  
Expression Patterns ◽  
Alternative Polyadenylation ◽  
Neuronal Identity ◽  
Relative Contribution ◽  
Stage Of Development ◽  
Neuronal Subtype ◽  
Definition Of ◽  
And Function ◽  
Type Specification

AbstractPrevious transcriptomic profiling studies have typically focused on separately analyzing mRNA expression, alternative splicing and alternative polyadenylation differences between cell and tissue types. However, the relative contribution of these three transcriptomic regulatory layers to cell type specification is poorly understood. This question is particularly relevant to neurons, given their extensive heterogeneity associated with brain location, morphology and function. In the present study, we generated profiles for the three regulatory layers from developmentally and regionally distinct subpopulations of neurons from the mouse hippocampus and broader nervous system. Multi-omics factor analyses revealed differing contributions of each transcriptomic layer in the discrimination of neurons based on their stage of development, region, and function. Importantly, profiles of differential alternative splicing and polyadenylation better discriminated specific neuronal subtype populations than gene expression patterns. These results provide evidence for differential relative contributions of coordinated gene regulatory layers in the specification of neuronal subtypes.

scholarly journals Specific alternative splicing and polyadenylation facilitate metastasis mediated by CTC clusters

2021 ◽  
Author(s):  
Wen Zhang ◽  
Quanyou Wu ◽  
Guoliang Li ◽  
Zhenrong Yang ◽  
Defeng Kong ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Posttranscriptional Regulation ◽  
Alternative Polyadenylation ◽  
Cell Types ◽  
Circulating Tumor Cell ◽  
Rna Regulation ◽  
Regulation Mechanisms ◽  
Specific Alternative ◽  
Single Ctcs

Abstract Circulating tumor cell (CTC) clusters possess a much higher capability to seed metastasis than single CTCs. However, the mechanism underlying this phenomenon is still elusive and no reports have investigated the role of posttranscriptional RNA regulation in CTC clusters. Here, we compared alternative splicing (AS) and alternative polyadenylation (APA) profiles between single CTCs and CTC clusters. 994 and 836 AS events were identified in single CTCs and CTC clusters, separately. About ~20% of AS events exhibited alterations between both cell types. The differential splicing of SRSF6 was a core event that caused AS profiles’ disturbance and made CTC clusters more dangerous. Concerning APA, we identified global 3’ UTRs lengthening in CTC clusters compared with single CTCs. This change was mainly regulated by 14 core APA factors, especially PPP1CA. The altered APA profiles boosted the cell cycle of CTC clusters and reflected that CTC clusters endured less oxidative stress. Our study investigated the posttranscriptional regulation mechanisms in CTC clusters, found that the perturbation of AS and APA contributed to the superiority of CTC clusters compared with single CTCs, and laid the foundation for developing antisense oligonucleotides that inhibit metastasis by reducing CTC clusters.

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