Abstract
Nucleosome depletion in the promoters has been indicated in yeasts, suggesting that nucleosome depletion in promoter might be a fundamental feature of eukaryotic transcriptional regulation. We compared the relationship between histone H3 acetylation at lysine 9 (K9) in promoter, gene expression level, and nucleosome density in the vicinity of the transcription start site (TSS), in HepG2 cells (human hepatocellular liver carcinoma cells). We found that the density of nucleosome is relatively low in the close vicinity of TSS flanked by H3 K9 significantly acetylated promoter, compared with that for genes without marked H3 K9 acetylation in promoter, regardless of their transcriptional activation status. Our results imply that the relative nucleosome depletion in the vicinity of TSS is not necessarily associated with active transcription, but with histone H3 K9 acetylation in promoter.
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Acknowledgements
We thank Tom Gingeras and his research group in Affymetrix, Affymetrix Japan, Harukazu Suzuki, Jun Kawai, and Haruhiko Koseki for helpful advice and useful suggestions. This work was supported in part by a Research Grant for the Genome Network Project and a Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government, a Research Grant for Advanced and Innovational Research Program in Life Science, and the Strategic Programs for R&D of Riken to Y.H.
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Nishida, H., Suzuki, T., Kondo, S. et al. Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res 14, 203–211 (2006). https://doi.org/10.1007/s10577-006-1036-7
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DOI: https://doi.org/10.1007/s10577-006-1036-7