Gene Expression Level and Gene Set Enrichment Analysis of Host Genes

Genome-wide analysis has shown that there are non-protein-coding RNAs (ncRNAs) that are localized on intronic regions of protein-coding genes. The intronic ncRNAs are hosted in introns of protein-coding genes that are referred to as host genes. Our previous study reported genomic features of intronic ncRNA genes and host genes. However, transcriptomic features of host genes have not been investigated. Here we report gene expression level analysis of host genes and investigate biological functions of host genes. Our results showed that gene expression levels of host genes tend to be higher than those of non-host genes. Host genes orthologous between human and mouse have more conserved expression levels than non-host orthologous genes. And host genes with high expression levels involve nervous system, gene expression, protein modification and cytoskeleton whereas there were mostly no enriched biological functions in host genes with low expression levels. These results suggest that host genes have characteristic transcript quantification and biological functions. The characteristics may be useful for further analysis of regulatory ways of host gene expression.

Intronic ncRNAs are in an intragenic region of a protein-coding gene. The intronic ncRNAs are expressed with the proteincoding genes. This inclusive relationship of genes is useful to estimate biological functions of intronic ncRNAs. Our previous study showed that host genes are conserved between species if the intronic ncRNA sequences are conserved and host genes involve specific biological functions. However, we have not analyzed transcriptomic features of host genes. In order to analyze baseline gene expression, we used RNA-seq data from a variety of healthy cells in human and mouse. The results showed that distributions of expression levels of host genes are not much different among tissues. We then compared expression levels of host genes with those of non-host genes. The comparison showed that expression levels of host genes tend to be higher than those of non-host genes at the most frequent values. This tendency was also observed in expression levels of host and non-host genes in mouse. These results suggest that host genes tend to be high expression levels in human and mouse. We also compared host genes orthologous between human and mouse. The results showed that correlation coefficients of orthologous host genes tend to be larger than those of orthologous non-host genes. This result suggests that expression levels of host genes are more conserved than nonhost genes in human and mouse

In conclusion, this study found that gene expression levels are slightly different between host and non-host genes and biological functions of host genes are different between high and low expression levels. These results are useful for further investigation of transcriptomic features of host genes. In future works, we will analyze gene expression difference of host genes and also investigate transcriptional regulation of host genes by using regulatory regions of host genes to predict and

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