Analysis of nucleosome positioning in promoters of miRNA genes and protein-coding genes

Abstract

Nucleosome positioning in promoters is important for gene transcription regulation. In this paper, with a nucleosome prediction model, curvature profile, the characteristics of nucleosome positioning in promoters are analyzed for miRNA genes and protein-coding genes. In the vicinity of transcription start site (TSS), there is a nucleosome-free region (NFR) followed by a positioned nucleosome at ∼200 bp downstream of TSS. A similar characteristic is observed in independent intronic promoters and intergenic promoters, namely, both types of promoters have a longer NFR in 0–−400 bp upstream of TSS. Moreover, transcription factor binding sites (TFBSs) locate in the NFR with a high concentration. However, nucleosome pattern in dependent intronic promoters are like that in protein-coding promoters, with two nucleosomes positioned at −200–−400 bp and −400–−600 bp upstream of TSS. The results indicate nucleosome positioning is probably different in independent miRNA promoters and protein-coding promoters; and positioning seems to be an important factor not only in regulation of protein-coding gene, but also in that of miRNA gene.