Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.

Xiaoyong Sun,Xiaoyan Yan,Simon M Lin

doi:10.1155/2014/736798

Abstract

NAGNAG alternative splicing plays an essential role in biological processes and represents a highly adaptable system for posttranslational regulation of gene function. NAGNAG alternative splicing impacts a myriad of biological processes. Previous studies of NAGNAG largely focused on messenger RNA. To the best of our knowledge, this is the first study testing the hypothesis that NAGNAG alternative splicing is also operative in large intergenic noncoding RNA (lincRNA). The RNA-seq data sets from recent deep sequencing studies were queried to test our hypothesis. NAGNAG alternative splicing of human lincRNA was identified while querying two independent RNA-seq data sets. Within these datasets, 31 NAGNAG alternative splicing sites were identified in lincRNA. Notably, most exons of lincRNA containing NAGNAG acceptors were longer than those from protein-coding genes. Furthermore, presence of CAG coding appeared to participate in the splice site selection. Finally, expression of the isoforms of NAGNAG lincRNA exhibited tissue specificity. Together, this study improves our understanding of the NAGNAG alternative splicing in lincRNA.

Highlights

The NAGNAG alternative splicing mechanism is a process which facilitates alternative protein expression from a single gene
Based on this observation of NAGNAG acceptors in Arabidopsis, we proposed an expanded paradigm and hypothesized that NAGNAG alternative splicing mechanism exists in large intergenic noncoding RNA (lincRNA)
NAGNAG alternative splicing was identified in the past decade and is characterized by inclusion or exclusion of three nucleotides at 3󸀠 splice sites, resulting in substitutions in one or two amino acids in the protein products

Summary

Introduction

The NAGNAG alternative splicing mechanism is a process which facilitates alternative protein expression from a single gene. NAGNAG alternative splicing targets inclusion or exclusion of three nucleotides at 3󸀠 splice sites (Figure 1), effecting a change in one or two amino acids encoded in the final protein [2,3,4,5,6,7,8,9]. Previous studies have assumed NAGNAG acceptors function through the classical mRNA paradigm based on observation of altered coding for one or two amino acids in the proteincoding gene Based on this observation of NAGNAG acceptors in Arabidopsis, we proposed an expanded paradigm and hypothesized that NAGNAG alternative splicing mechanism exists in lincRNA

Methods

Results

Conclusion