scholarly journals RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus

2021 ◽  
Author(s):  
Kathrin Jansen ◽  
Noriko Shikama-Dorn ◽  
Moustafa Attar ◽  
Stefano Maio ◽  
Maria Lopopolo ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Thymic Epithelial Cells ◽  
Gene Repertoire ◽  
Loss Of Function ◽  
Cell Repertoire ◽  
Protein Coding ◽  
Peripheral Tissues ◽  
Small Set ◽  
Splice Isoform ◽  
Splicing Patterns

Thymic epithelial cells (TEC) control the selection of a T cell repertoire reactive to pathogens but tolerant of self. This process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire, but the extent to which TEC recapitulate peripheral isoforms, and the mechanisms by which they do so, remain largely unknown. We performed the first assembly-based transcriptomic census of transcript structures and splicing factor (SF) expression in mouse medullary TEC (mTEC) and 21 peripheral tissues. Mature mTEC expressed 60.1% of all protein-coding transcripts, more than was detected in any of the peripheral tissues. However, for genes with tissue-restricted expression, mTEC produced fewer isoforms than did the relevant peripheral tissues. Analysis of exon inclusion revealed an absence of brain-specific microexons in mTEC. We did not find unusual numbers of novel transcripts in TEC, and we show that Aire, the facilitator of promiscuous gene expression, promotes the generation of long “classical” transcripts (with 5′ and 3′ UTRs) but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of nonpromiscuously expressed SF genes, among which we confirmed RBFOX to be present with AIRE in mTEC nuclei. Using a conditional loss-of-function approach, we show that Rbfox2 promotes mTEC development and regulates the alternative splicing of promiscuously expressed genes. These data indicate that TEC recommission a small number of peripheral SFs, including members of the RBFOX family, to generate a broad but selective representation of the peripheral splice isoform repertoire.

scholarly journals Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells

2020 ◽  
Author(s):  
Kathrin Jansen ◽  
Noriko Shikama-Dorn ◽  
Moustafa Attar ◽  
Stefano Maio ◽  
Maria Lopopolo ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Splicing Factor ◽  
Thymic Epithelial Cells ◽  
Splicing Factors ◽  
Gene Repertoire ◽  
Cell Repertoire ◽  
Protein Coding ◽  
Peripheral Tissues ◽  
Splice Isoform ◽  
Self Antigen

AbstractThymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. Our results indicate that TEC re-use a small number of peripheral splicing factors to recreate a limited subset of the peripheral splice isoform repertoire. We found, for example, that TEC lacked both neuronal micro-exons and the splicing factor, Srrm4, which promotes their inclusion. We demonstrate a functional role for the Rbfox splicing factors in promoting medullary TEC development and the alternative splicing of promiscuously expressed genes. Our findings have implications for understanding autoimmune diseases and the development of antigen-specific immunotherapies.

scholarly journals Rbfox3-regulated alternative splicing of Numb promotes neuronal differentiation during development

2013 ◽  
Vol 200 (4) ◽  
pp. 443-458 ◽  
Author(s):  
Kee K. Kim ◽  
Joseph Nam ◽  
Yoh-suke Mukouyama ◽  
Sachiyo Kawamoto
Keyword(s):  
Alternative Splicing ◽  
Neuronal Differentiation ◽  
Rna Binding ◽  
Adaptor Protein ◽  
Gene Products ◽  
Vertebrate Development ◽  
Loss Of Function ◽  
Major Mechanism ◽  
Splice Isoform ◽  
Postmitotic Neurons

Alternative premRNA splicing is a major mechanism to generate diversity of gene products. However, the biological roles of alternative splicing during development remain elusive. Here, we focus on a neuron-specific RNA-binding protein, Rbfox3, recently identified as the antigen of the widely used anti-NeuN antibody. siRNA-mediated loss-of-function studies using the developing chicken spinal cord revealed that Rbfox3 is required to promote neuronal differentiation of postmitotic neurons. Numb premRNA encoding a signaling adaptor protein was found to be a target of Rbfox3 action, and Rbfox3 repressed the inclusion of an alternative exon via binding to the conserved UGCAUG element in the upstream intron. Depleting a specific Numb splice isoform reproduced similar neuronal differentiation defects. Forced expression of the relevant Numb splice isoform was sufficient to rescue, in an isoform-specific manner, postmitotic neurons from defects in differentiation caused by Rbfox3 depletion. Thus, Rbfox3-dependent Numb alternative splicing plays an important role in the progression of neuronal differentiation during vertebrate development.

scholarly journals Genetics of alternative splicing evolution during sunflower domestication

2018 ◽  
Vol 115 (26) ◽  
pp. 6768-6773 ◽  
Author(s):  
Chris C. R. Smith ◽  
Silas Tittes ◽  
J. Paul Mendieta ◽  
Erin Collier-zans ◽  
Heather C. Rowe ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Population Divergence ◽  
Evolutionary Transition ◽  
Differential Splicing ◽  
Evolutionary Transitions ◽  
Protein Coding ◽  
Standing Variation ◽  
Splice Forms ◽  
Splicing Patterns

Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarilytrans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wildHelianthus annuusand gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from otherHelianthusspecies. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.

scholarly journals Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 182 ◽  
Author(s):  
Muthusamy ◽  
Yoon ◽  
Kim ◽  
Jeong ◽  
Lee
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Stress Response ◽  
Drought Tolerance ◽  
Brassica Rapa ◽  
Target Genes ◽  
Tolerance Index ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Splicing Patterns

The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.

scholarly journals Aire-dependent transcripts escape H3K36me3 and Raver2 induced alternative splicing to sustain central immune tolerance

2021 ◽  
Author(s):  
Francine Padonou ◽  
Virginie Gonzalez ◽  
Nada Jmari ◽  
Julia Maslovskaja ◽  
Kai Kisand ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Negative Selection ◽  
Thymic Epithelial Cells ◽  
Related Factor ◽  
Splice Isoforms ◽  
Peripheral Tissues ◽  
Central Tolerance ◽  
Medullary Thymic Epithelial Cells ◽  
Self Antigen ◽  
High Diversity

AbstractAire allows medullary thymic epithelial cells (mTECs) to express and present a large number of self-antigens for central tolerance. Although mTECs express a high diversity of self-antigen splice isoforms, the extent and regulation of alternative splicing events (ASEs) included in their transcripts, notably in those induced by Aire, is unknown. Unexpectedly, and in contrast to Aire-neutral genes, we found that the Aire-sensitive genes exhibit in Aire-positive and negative mTECs, a weak inclusion of ASEs, with about a quarter present in peripheral tissues being excluded from the thymus. We identified Raver2, as a splicing-related factor overrepresented in mTECs and dependent on H3K36me3 marks. We discovered that both Raver2 and methylation of H3K36 promoted ASE inclusion for Aire-neutral genes, leaving Aire-sensitive genes unaffected. Profiling of H3K36me3 revealed its depletion at Aire-sensitive genes, supporting a mechanism, whose setup precedes Aire’s expression and by which Aire-sensitive genes exhibit weak ASE inclusion through the escape of Raver2’s effect. Lack of ASEs in Aire-induced transcripts highlights a role for regulatory T cells in controlling the incomplete Aire-dependent negative selection.

LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers

2020 ◽  
Author(s):  
Yulan Deng ◽  
Hao Luo ◽  
Zhenyu Yang ◽  
Lunxu Liu
Keyword(s):  
Alternative Splicing ◽  
Rna Sequencing ◽  
Protein Coding ◽  
Functional Roles ◽  
Comprehensive Database ◽  
Human Cancers ◽  
Manual Curation ◽  
Annotation Information ◽  
Cancer Types ◽  
Splicing Patterns

Abstract Accumulating studies demonstrated that the roles of lncRNAs for tumorigenesis were isoform-dependent and their aberrant splicing patterns in cancers contributed to function specificity. However, there is no existing database focusing on cancer-related alternative splicing of lncRNAs. Here, we developed a comprehensive database called LncAS2Cancer, which collected 5335 bulk RNA sequencing and 1826 single-cell RNA sequencing samples, covering over 30 cancer types. By applying six state-of-the-art splicing algorithms, 50 859 alternative splicing events for 8 splicing types were identified and deposited in the database. In addition, the database contained the following information: (i) splicing patterns of lncRNAs under seven different conditions, such as gene interference, which facilitated to infer potential regulators; (ii) annotation information derived from eight sources and manual curation, to understand the functional impact of affected sequences; (iii) survival analysis to explore potential biomarkers; as well as (iv) a suite of tools to browse, search, visualize and download interesting information. LncAS2Cancer could not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones. Using the data deposited in LncAS2Cancer, we compared gene model and transcript overlap between lncRNAs and protein-coding genes and discusses how these factors, along with sequencing depth, affected the interpretation of splicing signals. Based on recurrent signals and potential confounders, we proposed a reliable score to prioritize splicing events for further elucidation. Together, with the broad collection of lncRNA splicing patterns and annotation, LncAS2Cancer will provide important new insights into the diverse functional roles of lncRNA isoforms in human cancers. LncAS2Cancer is freely available at https://lncrna2as.cd120.com/.

scholarly journals Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity

2017 ◽  
Author(s):  
Timothy Sterne-Weiler ◽  
Robert J. Weatheritt ◽  
Andrew Best ◽  
Kevin C. H. Ha ◽  
Benjamin J. Blencowe
Keyword(s):  
Alternative Splicing ◽  
Significant Loss ◽  
Rna Seq ◽  
Accurate Analysis ◽  
Splice Isoforms ◽  
Protein Coding ◽  
High Entropy ◽  
Normal Tissues ◽  
Splicing Patterns ◽  
Entropic Measure

AbstractAlternative splicing (AS) is a widespread process underlying the generation of transcriptomic and proteomic diversity in metazoans. Major challenges in comprehensively detecting and quantifying patterns of AS are that RNA-seq datasets are expanding near exponentially, while existing analysis tools are computationally inefficient and ineffective at handling complex splicing patterns. Here, we describe Whippet, a method that rapidly, and with minimal hardware requirements, models and quantifies splicing events of any complexity without significant loss of accuracy. Using an entropic measure of splicing complexity, Whippet reveals that approximately 33% of human protein coding genes contain complex AS events that result in substantial expression of multiple splice isoforms. These events frequently affect tandem arrays of folded protein domains. Remarkably, high-entropy AS events are more prevalent in tumour relative to matched normal tissues, and these differences correlate with increased expression of proto-oncogenic splicing factors. Whippet thus affords the rapid and accurate analysis of AS events of any complexity, and as such will facilitate biomedical research.

scholarly journals PPM1G promotes the progression of hepatocellular carcinoma via phosphorylation regulation of alternative splicing protein SRSF3

2021 ◽  
Vol 12 (8) ◽  
Author(s):  
Dawei Chen ◽  
Zhenguo Zhao ◽  
Lu Chen ◽  
Qinghua Li ◽  
Jixue Zou ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Alternative Splicing ◽  
Protein Function ◽  
Vital Role ◽  
Normal Tissues ◽  
Mechanistic Analysis ◽  
Highly Correlated ◽  
Splicing Patterns

AbstractEmerging evidence has demonstrated that alternative splicing has a vital role in regulating protein function, but how alternative splicing factors can be regulated remains unclear. We showed that the PPM1G, a protein phosphatase, regulated the phosphorylation of SRSF3 in hepatocellular carcinoma (HCC) and contributed to the proliferation, invasion, and metastasis of HCC. PPM1G was highly expressed in HCC tissues compared to adjacent normal tissues, and higher levels of PPM1G were observed in adverse staged HCCs. The higher levels of PPM1G were highly correlated with poor prognosis, which was further validated in the TCGA cohort. The knockdown of PPM1G inhibited the cell growth and invasion of HCC cell lines. Further studies showed that the knockdown of PPM1G inhibited tumor growth in vivo. The mechanistic analysis showed that the PPM1G interacted with proteins related to alternative splicing, including SRSF3. Overexpression of PPM1G promoted the dephosphorylation of SRSF3 and changed the alternative splicing patterns of genes related to the cell cycle, the transcriptional regulation in HCC cells. In addition, we also demonstrated that the promoter of PPM1G was activated by multiple transcription factors and co-activators, including MYC/MAX and EP300, MED1, and ELF1. Our study highlighted the essential role of PPM1G in HCC and shed new light on unveiling the regulation of alternative splicing in malignant transformation.

scholarly journals LINC01089 functions as a ceRNA for miR-152-3p to inhibit non‐small lung cancer progression through regulating PTEN

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huixian Zhang ◽  
Hao Zhang ◽  
Xingya Li ◽  
Siyuan Huang ◽  
Qianqian Guo ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Progression ◽  
Expression Level ◽  
Cell Counting ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Loss Of Function ◽  
Protein Coding ◽  
Tensin Homolog ◽  
Pten Mrna

Abstract Background Long non-coding RNAs (lncRNAs) have been reported to exert crucial functions in regulating the progression of human cancers. However, the function and mechanism of long intergenic non-protein coding RNA 01089 (LINC01089) in non-small cell lung cancer (NSCLC) have not been revealed. Methods The expression level of LINC01089, microRNA (miRNA, miR)-152-3p and phosphatase and tensin homolog deleted onc hromosome ten (PTEN) mRNA was detected by quantitative real-time PCR (qRT-PCR). After gain-of-function and loss-of-function models were established with NSCLC cell lines, the proliferation, migration and invasion of NSCLC cells were detected by cell counting kit-8 (CCK-8) assay, scratch healing assay, Transwell assay, respectively. Dual luciferase reporter assay was employed to validate the binding relationship between miR-152-3p and LINC01089 or the 3’UTR of PTEN. Western blot was used to detect PTEN expression in NSCLC cells after LINC01089 and miR-152-3p were selectively modulated. Results LINC01089 was down-regulated in NSCLC tissues and cells. Functional experiments showed that knockdown of LINC01089 could promote the proliferation, migration and invasion of NSCLC cells, while over-expression of LINC01089 had the opposite effects. miR-152-3p was identified as a functional target for LIN01089, and miR-152-3p could reverse the function of LINC01089. Additionally, LINC01089 could up-regulate the expression level of PTEN via repressing miR-152-3p. Conclusions Down-regulation of LINC01089 promoted the progression of NSCLC through regulating miR-152-3p/PTEN axis.

Sign in / Sign up

Export Citation Format

Share Document