Comparative Analysis of Intronic Noncoding RNA Genes among Organisms

Development of sequencing techniques allowed us to determine genomic sequences in many organisms. Such a determined genome consists of not only protein-coding genes but also noncoding RNA (ncRNA) genes. We should analyze evolutional histories of such genes to estimate evolutional directions in future. Meanwhile, recent studies showed that some ncRNA genes are located in intragenic regions in protein-coding genes, which are called host genes. We considered that such information can help us to discuss gene evolutions. In this study, we constructed a database to analyze evolutions of protein-coding and noncoding genes based on gene locations in genomic sequences. We found that 547 out of 2,691 human host genes are orthologous to 546 out of 1,633 mouse host genes. Such orthologous host genes are involved in similar biological functions but some non-orthologous host genes have different functions. For example, non-orthologous host genes in human are annotated as neuron-related terms but such genes in mouse are not. Meanwhile, similarity searches for intronic microRNA (miRNA) genes between human and mouse showed that 85 out of the orthologous host genes have retained miRNA genes in the intronic regions. 64 out of such genes have retained intronic miRNA genes among human, mouse and rat. These results suggest that some orthologous genes have retained ncRNA genes in the intronic regions in the evolutionary process.