Functional analysis of repeat regions in the eukaryotic genomes: functional analysis of repetitive DNA derived from transposable elements in the human genome

Abstract

Nearly half of the human genome is made up of transposable elements (TEs). With the rapid progress of sequencing technologies, we are now much better able to systematically analyze these TEs. We have used multiple types of omics data, including the genomic sequences, epigenetic data and transcriptomic data, to investigate the potential functions of TEs across the entire human genome. Comparative analysis revealed that a large proportion of potentially functional transposable elements were located in introns, and they were mainly associated with gene repression. Functional classification from GO enrichment showed that different functions were enriched in protein coding regions containing TEs compared to non-protein coding regions. For example, protein coding genes with Alus in non-coding regions are enriched with respect to intracellular membrane-bounded organelles, while protein coding genes with Alus in coding regions are more enriched at intracellular non-membrane-bounded organelles. Significantly, transcriptome data showed that the genes with TEs had lower expression levels compared with genes without TEs, revealing a novel aspect of the impact of TEs on the human genome. In addition, genome wide analysis of repeats with regulatory elements showed that MIR and L2 repeats were more probable to be active regulators while L1 repeats were less probable to be regulators. In conclusion, the role of TEs is significant across the genome. Repeats reduce or repress the expression of related gene, either through the proximal promoter, 5’UTR or 3’UTR or perhaps as components of lincRNA exons.