2005 August 11 | Tae Hoon Kim, Leah O. Barrera, Ming Zheng, Chunxu Qu, Michael A. Singer, Todd A. Richmond, Yingnian Wu, Roland D. Green, Bing Ren
This study presents a high-resolution map of active promoters in human fibroblast cells, determined by chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-on-chip). The map identifies 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 unannotated transcriptional units. Key findings include extensive usage of multiple promoters by human genes and widespread clustering of active promoters in the genome. Four general classes of promoters are identified based on genome-wide expression profiles, providing insights into the functional relationship between transcriptional machinery, chromatin structure, and gene expression. The study also highlights the significance of CpG islands in gene expression and the absence of the TATA box as a common promoter motif in human genes. Additionally, the analysis reveals that many genes contain multiple promoters, indicating a greater complexity in the cellular proteome and coordinated regulation of transcriptional initiation, splicing, and polyadenylation. The results provide a framework for understanding cis-regulatory logic in human cells and suggest that further analysis of additional cell types will help elucidate the control logic governing gene expression in different tissues.This study presents a high-resolution map of active promoters in human fibroblast cells, determined by chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-on-chip). The map identifies 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 unannotated transcriptional units. Key findings include extensive usage of multiple promoters by human genes and widespread clustering of active promoters in the genome. Four general classes of promoters are identified based on genome-wide expression profiles, providing insights into the functional relationship between transcriptional machinery, chromatin structure, and gene expression. The study also highlights the significance of CpG islands in gene expression and the absence of the TATA box as a common promoter motif in human genes. Additionally, the analysis reveals that many genes contain multiple promoters, indicating a greater complexity in the cellular proteome and coordinated regulation of transcriptional initiation, splicing, and polyadenylation. The results provide a framework for understanding cis-regulatory logic in human cells and suggest that further analysis of additional cell types will help elucidate the control logic governing gene expression in different tissues.