Abstract
BackgroundHistone 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.ResultsWe 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.ConclusionsClustering 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.
Highlights
Histone modifications play an important role in gene regulation
Figure 1(A) shows H3K9 acetylation and gene transcription start sites in ENCODE region ENr333 as an example of how H3K9ac is concentrated around DeepCAGE promoters and gene starts
These results suggest that there are several different typical acetylation states, as depicted in Figure 4: while in all three clusters broad promoters are most prevalent (Figure 4(B, C, D)), single peak promoters still occur in more than 40% of the cases where the H3K9ac signal is concentrated in the upstream region (Figure 4(A))
Summary
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. Even the same type of modification, on the same histone and residue, can be activating or repressing depending on the underlying sequence context; for example, methylation of H3K36 is enhancing transcription if the affected histone resides in the coding region of a gene, but it is a repressing mark in the promoter region [5]. Acetylation can function locally, being restricted to short sequences of the genome, where it is associated with upregulated transcription of individual genes [5] It is currently not understood if the formation of euchromatin and locally accessible regions on one hand, and heterochromatin and locally inaccessible regions on the other hand, are results of active gene transcription or if gene transcription is activated and suppressed as a result of the histone modification state
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
