Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, Carsten O. Daub

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Background: Histone modifications play an important role in gene regulation. Acetylation of histone 3 lysine 9 (H3K9ac) is generally associated with transcription initiation and unfolded chromatin, thereby positively influencing gene expression. Deep sequencing of the 5' ends of gene transcripts using DeepCAGE delivers detailed information about the architecture and expression level of gene promoters. The combination of H3K9ac ChIP-chip and DeepCAGE in a myeloid leukemia cell line (THP-1) allowed us to study the spatial distribution of H3K9ac around promoters using a novel clustering approach. The promoter classes were analyzed for association with relevant genomic sequence features.Results: We performed a clustering of 4,481 promoters according to their surrounding H3K9ac signal and analyzed the clustered promoters for association with different sequence features. The clustering revealed three groups with major H3K9ac signal upstream, centered and downstream of the promoter. Narrow single peak promoters tend to have a concentrated activity of H3K9ac in the upstream region, while broad promoters tend to have a concentrated activity of H3K9ac and RNA polymerase II binding in the centered and downstream regions. A subset of promoters with high gene expression level, compared to subsets with low and medium gene expression, shows dramatic increase in H3K9ac activity in the upstream cluster only; this may indicate that promoters in the centered and downstream clusters are predominantly regulated at post-initiation steps. Furthermore, the upstream cluster is depleted in CpG islands and more likely to regulate un-annotated genes.Conclusions: Clustering core promoters according to their surrounding acetylation signal is a promising approach for the study of histone modifications. When examining promoters clustered into groups according to their surrounding H3K9 acetylation signal, we find that the relative localization and intensity of H3K9ac is very specific depending on characteristic sequence features of the promoter. Experimental data from DeepCAGE and ChIP-chip experiments using undifferentiated (monocyte) and differentiated (macrophage) THP-1 cells leads us to the same conclusions.

Original languageEnglish
Article number257
JournalBMC Genomics
Volume11
Issue number1
DOIs
Publication statusPublished - 2010 Apr 21

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Acetylation
Histones
Lysine
Cluster Analysis
Histone Code
Gene Expression
Genes
High-Throughput Nucleotide Sequencing
CpG Islands
Myeloid Leukemia
RNA Polymerase II
Myeloid Cells
Chromatin
Monocytes
Macrophages
Cell Line

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Kratz, A., Arner, E., Saito, R., Kubosaki, A., Kawai, J., Suzuki, H., ... Daub, C. O. (2010). Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC Genomics, 11(1), [257]. https://doi.org/10.1186/1471-2164-11-257

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. / Kratz, Anton; Arner, Erik; Saito, Rintaro; Kubosaki, Atsutaka; Kawai, Jun; Suzuki, Harukazu; Carninci, Piero; Arakawa, Takahiro; Tomita, Masaru; Hayashizaki, Yoshihide; Daub, Carsten O.

In: BMC Genomics, Vol. 11, No. 1, 257, 21.04.2010.

Research output: Contribution to journalArticle

Kratz, A, Arner, E, Saito, R, Kubosaki, A, Kawai, J, Suzuki, H, Carninci, P, Arakawa, T, Tomita, M, Hayashizaki, Y & Daub, CO 2010, 'Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns', BMC Genomics, vol. 11, no. 1, 257. https://doi.org/10.1186/1471-2164-11-257
Kratz, Anton ; Arner, Erik ; Saito, Rintaro ; Kubosaki, Atsutaka ; Kawai, Jun ; Suzuki, Harukazu ; Carninci, Piero ; Arakawa, Takahiro ; Tomita, Masaru ; Hayashizaki, Yoshihide ; Daub, Carsten O. / Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
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