Chapter 11 - Are transposable elements enemies within?

Abstract

In previous chapters, we have reviewed 5’-upstream flanking regions of various human genes, including protein coding and noncoding genes. It has been shown that many mitochondrial function, DNA repair, histone H2As, and immune response-associated factor encoding genes have head-head linked bidirectional partner genes. In contrast, majority of the genes encoding glycolysis enzymes, and histone-modifying and DNA methylation factors are, in general, transcribed unidirectionally or tail-head linked with other genes. To better understand the order of genes in human genomes, we might recall genomic regions or structures where rRNAs and tRNAs transcription occurs. Moreover, given that mitochondria have evolved from the symbiosis of aerobic ancestor(s), prokaryotic gene structures may give us a hint towards resolving the question of why most mitochondrial function-associated genes have bidirectional head-head linked partner genes. In addition, we might discuss a mechanism(s) that contributes to the integration of the mitochondrial ancestral genes into eukaryotic cells. This might be explained by the systems of integration of retroviral genomes. In general, although transposing activities are not so strong in the human genome, it has been shown that many transposable elements, including long interspersed element-1s (LINE-1s) and short interspersed elements (SINEs) are identified and characterized in human genomes. In this chapter, before discussing the molecular mechanisms that made bidirectional promoters in the human genome, we will review the characters of jumping (but not merely junk) DNAs.