期刊
CELL CYCLE
卷 8, 期 24, 页码 4127-4137出版社
TAYLOR & FRANCIS INC
DOI: 10.4161/cc.8.24.10240
关键词
CCAAT; NF-Y; promoter; PSFM
类别
资金
- AIRC
- PRIN-MIUR
- CARIPLO-Nobel
- FIRB-MIUR
The CCAAT box is an important promoter element regulated by NF-Y, a conserved trimer with histone-like features. We describe a new Position Specific Frequency Matrix (PSFM): we derived from 328 NF-Y promoters from the literature the p-CCAAT, and refined it by analysing ChIP on chip data (g-CCAAT). Interestingly, g-CCAAT has distinct features, such as variations within the CCAAT pentanucleotide. We validated the NF-Y-dependency of several promoters with functional assays. We examined the presence of these PSFMs in all human promoters and detail a number of parameters of CCAAT boxes: position, orientation, distance from TSS, presence of TATA, CpG islands and enrichments of nearby TF elements. The CCAAT genes fall into different GO categories, with cell cycle and chromatin/transcription specifically enriched. Additional findings surfaced: (1) the CCAAT-TATA combination, often mentioned in textbooks, is an exception, rather than the rule. CCAAT promoters are less precise in terms of TSS; (2) There is a good correlation between CCAAT and CpG islands; (3) selective TFs sites are enriched in CCAAT promoters, with precise stereoalignements of some of them. In conclusion, the new features of the CCAAT box and the link with the neighbouring elements will help in the functional classification of promoters.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据