Gene Expression Profiles Controlled by the Alternative Splicing Factor Nova2 in Endothelial Cells.

Elisa Belloni,Christopher D R Wyatt,Simone Sabbioneda,Claudia Ghigna,Antonio Maffia,Anna Di Matteo,Margherita Vacca,Roberta Alfieri,Davide Pradella

doi:10.3390/cells8121498

Abstract

Alternative splicing (AS) plays an important role in expanding the complexity of the human genome through the production of specialized proteins regulating organ development and physiological functions, as well as contributing to several pathological conditions. How AS programs impact on the signaling pathways controlling endothelial cell (EC) functions and vascular development is largely unknown. Here we identified, through RNA-seq, changes in mRNA steady-state levels in ECs caused by the neuro-oncological ventral antigen 2 (Nova2), a key AS regulator of the vascular morphogenesis. Bioinformatics analyses identified significant enrichment for genes regulated by peroxisome proliferator-activated receptor-gamma (Ppar-γ) and E2F1 transcription factors. We also showed that Nova2 in ECs controlled the AS profiles of Ppar-γ and E2F dimerization partner 2 (Tfdp2), thus generating different protein isoforms with distinct function (Ppar-γ) or subcellular localization (Tfdp2). Collectively, our results supported a mechanism whereby Nova2 integrated splicing decisions in order to regulate Ppar-γ and E2F1 activities. Our data added a layer to the sequential series of events controlled by Nova2 in ECs to orchestrate vascular biology.

Highlights

Alternative splicing (AS), which generates different mature transcripts from a single gene, is recognized to play a prominent role in expanding the coding potential of the human genome through the generation of specialized protein variants required in precise cellular processes, tissues, or developmental stages [1]
In order to better characterize neuro-oncological ventral antigen 2 (Nova2) functions in vascular endothelium, we investigated changes in the whole transcriptome after its knockdown in endothelial cell (EC), identifying novel molecular pathways regulated by this splicing regulatory factors (SRFs), which could play a relevant role to orchestrate EC biology and vascular development
In order to comprehensively identify genes with AS events modulated by Nova2 in the endothelium, we previously used RNA-seq of stable Nova2 knockdown and control ECs derived from mouse embryos (Supplementary Figure S1A)

Summary

Introduction

Alternative splicing (AS), which generates different mature transcripts (mRNAs) from a single gene, is recognized to play a prominent role in expanding the coding potential of the human genome through the generation of specialized protein variants required in precise cellular processes, tissues, or developmental stages [1]. A number of SRFs function themselves as oncogenes [8,9] or tumor suppressors [10,11], generating cancer-associated AS proteins involved in almost all aspects of tumor cell biology [4]. Aberrant AS is recognized as another hallmark of cancer [12,13], and cancer-associated AS isoforms can be used to stratify patients for cancer diagnosis or as predictive biomarkers of prognosis [14,15]. Their targeting can be exploited to improve the development of novel anti-cancer therapies [6,12]

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Results

Conclusion