Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

Tanya Vavouri,Ben Lehner

doi:10.1186/gb-2012-13-11-r110

Abstract

BackgroundMore than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications.ResultsHere we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. This signature includes high levels of the transcription elongation-associated histone modifications H4K20me1, H2BK5me1 and H3K79me1/2/3 in the 5' end of the gene, depletion of the activation marks H2AK5ac, H3K14ac and H3K23ac immediately downstream of the transcription start site (TSS), and characteristic epigenetic asymmetries around the TSS. The chromosome organization factor CTCF may be bound upstream of RNA polymerase in most active CpG island promoters, and an unstable nucleosome at the TSS may be specifically marked by H4K20me3, the first example of such a modification. H3K36 monomethylation is only detected as enriched in the bodies of active genes that have CpG island promoters. Finally, as expression levels increase, peak modification levels of the histone methylations H3K9me1, H3K4me1, H3K4me2 and H3K27me1 shift further away from the TSS into the gene body.ConclusionsThese results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription-associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates.

Highlights

More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands
Chromatin profile comparison of expression-matched genes with and without CpG islands in their promoters To test whether human genes with CpG island promoters have a distinct chromatin organization, we analyzed the levels of histone modifications and other epigenetic modifications in 1,500 CpG and 1,500 non-CpG promoter genes with precisely matched expression levels (Materials and methods; Figure 1a; Additional files 1 and 2)
Transcription is a strong influence on chromatin organization [24,33,35,36,37,38,39] and so it is necessary to control for expression level when examining additional potential influences

Summary

Introduction

More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications. More than half of human genes initiate transcription from regions of the genome with an elevated content of CpG dinucleotides and G+C base pairs referred to as ‘CpG islands’ [1,2]. In contrast to the rest of the genome, where CpG dinucleotides are heavily methylated and so rapidly lost through deamination, CpG sites within promoter CpG islands are normally free from DNA methylation and do not have an elevated mutation rate [3,4,5,6,7]. CpG promoters are less likely to contain a TATAbox [13], and contain fewer located transcription factor binding sites [20]

Results

Discussion

Conclusion