Nucleosome Positioning of Intronless Genes in the Human Genome

Abstract

Nucleosomes, the basic units of chromatin, are involved in transcription regulation and DNA replication. Intronless genes, which constitute 3 percent of the human genome, differ from intron-containing genes in evolution and function. Our analysis reveals that nucleosome positioning shows a distinct pattern in intronless and intron-containing genes. The nucleosome occupancy upstream of transcription start sites of intronless genes is lower than that of intron-containing genes. In contrast, high occupancy and well positioned nucleosomes are observed along the gene body of intronless genes, which is perfectly consistent with the barrier nucleosome model. Intronless genes have a significantly lower expression level than intron-containing genes and most of them are not expressed in CD4+ T cell lines and GM12878 cell lines, which results from their tissue specificity. However, the highly expressed genes are at the same expression level between the two types of genes. The highly expressed intronless genes require a higher density of RNA Pol II in an elongating state to compensate for the lack of introns. Additionally, 5' and 3' nucleosome depleted regions of highly expressed intronless genes are deeper than those of highly expressed intron-containing genes.