A systematic view on mobile elements’ contribution to human transcriptomes

Abstract

Mobile elements (MEs) are a major component in most higher eukaryotic genomes. MEs account over 50% of the human genome and consist of long interspersed elements (LINEs), Short interspersed elements (SINEs), and SINE-VNTR-Alu (SVAs) and long terminal repeats (LTR). MEs are known to play important roles in genome evolution and gene function and their roles include but are not limited to the generation of alternative splicing, insertional mutations, genomic instability and epigenetic regulation. Nevertheless, a systematic analysis of MEs contribution to transcriptomes in humans has not been conducted. In this study, we examined the MEs’ participation in the human reference transcriptome and the transcriptomes of many human tissues. Our results show that MEs contribute to 16% to the human reference transcriptome and on average ~24% to the full transcriptomes of human tissues. MEs’ contribution to human full transcriptomes varies from tissue to tissues and from person to person. MEs contribute to all exon features, but 60% of them are in non-coding regions. Also, they contribute to the transcripts of 4,402 protein coding genes, including regions, which are conserved among primates, mammals, and even vertebrates. We noticed that while Alus are the most prominent contributors to human transcriptomes involving mostly alternative transcripts, SVAs as the youngest ME class showed most active participation in protein coding genes with 78% contributing to the canonical transcripts. Furthermore, MEs also participate in post-transcriptional regulation by contributing to the formation of 16% miRNAs, ~9% of miRNA target sites, and at least 2,921 double stranded RNA sites for RNA-editing. In conclusion, our data demonstrate that MEs are very active participants in human transcriptomes by contributing to both non-coding RNAs and protein coding transcripts and to post-transcriptional regulation via miRNA and RNA-editing.