RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

Abstract

Background: Alternative splicing, a ubiquitous phenomenon in eukaryotes, provides a regulatory mechanism for the biological diversity of individual genes.Most studies have focused on the e↵ects of alternative splicing for protein synthesis. However, the influence of alternative splicing on the RNA subcellular localization has rarely been studied.Results: By analyzing RNA-seq data from subcellular fractions across thirteen human cell lines, we observed that splicing is apparent to promote cytoplasmic localization. We also discovered that intron retention is preferred by transcripts localized in the nucleus. Short and structurally stable introns show a positive correlation with nuclear localization. Such introns are predicted to be preferentially bound by MBNL1, an RNA-binding protein that contains two nuclear localization signals.Conclusions: Our findings reveal that alternative splicing plays an important role in regulating RNA subcellular localization. This study provides valuable clues for understanding the biological mechanisms of alternative splicing. 1 2 3Most eukaryotic genes consist of exons (encoding mature RNAs) and introns (re-4 moved by RNA splicing). Alternative splicing is known as a regulated process by 5 which exons can be either included or excluded. Various RNAs (also called transcript 6 variants) can be produced from a single gene through alternative splicing. Thus, al-7 ternative splicing enables a cell to express more RNA species with a limited number 8 of genes, which increases the genome complexity [1]. In humans, for instance, about 95% of the multi-exonic genes undergoing alternative splicing were uncovered by 1 high-throughput sequencing technology [2]. Exploring the functionality of alterna-2 tive splicing is critical to our understanding of life mechanisms. Alternative splicing 3 has been reported to be associated with protein functions, such as diversification, 4 molecular binding properties, catalytic and signaling abilities, and stability. Such 5 related studies have been reviewed elsewhere [3, 4]. Additionally, relationships be-6 tween alternative splicing and disease [5] or cancer [6, 7] has received increasing 7 attention. Understanding the pathogenesis associated with alternative splicing can 8 shed light on diagnosis and therapy. With the emergence and rapid development 9 of high-throughput technology, it has become possible to study the function and 10 mechanism of alternative splicing genome-wide [8]. 11The location of an RNA in a cell can determine whether the RNA is translated, 12 preserved, modified, or degraded [9, 10]. In other words, the subcellular location of 13 an RNA is highly related to its biological function [9]. For example, the asymmetric 14 distribution of RNA in cells can influence the expression of genes [9], the forma-15 tion and interaction of protein complexes [11], the biosynthesis of ribosomes [12],the 16 development of cells [13, 14], among other functions. Many techniques have been de-17 veloped to investigate the subcellular localization of RNAs. RN...