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

作　　者：LIU HongDe ZHANG DeJin XIE JianMing YUAN ZhiDong MA Xin LU ZhiYuan GONG LeJun SUN Xiao 

机构地区：[1]State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China

出　　处：《Chinese Science Bulletin》2010年第22期2347-2352,共6页

基　　金：supported by the National Natural Science Foundation of China (60671018 and 30800209)

摘　　要：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.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.

关 键 词：蛋白编码基因 基因启动子 核小体 点定位 RNA基因 miRNA 蛋白质编码 转录起始位点 

分 类 号：Q753[生物学—分子生物学] Q754