Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome

Shicai Fan,Michael Q Zhang,Fang Fang,Xuegong Zhang,Jörg Hoheisel

doi:10.1371/journal.pone.0001184

Abstract

BackgroundMajority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor.Methodology/Principal FindingsUsing the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of methylation-resistant CpG islands, and discovered that there are several over-represented putative Transcription Factor Binding Sites (TFBSs) in methylation-resistant CpG islands, and a specific group of zinc finger protein binding sites are over-represented in boundary regions (∼400 bp) flanking such CpG islands. About 77% of the over-represented putative TFBSs are conserved among human, mouse and rat. We also observed the enrichment of 4 histone methylations in methylation-resistant CpG islands or their boundaries.Conclusions/SignificanceOur results suggest a possible mechanism that certain putative zinc finger protein binding sites over-represented in the boundary regions of the methylation-resistant CpG islands may block the spreading of methylation into these islands, and those TFBSs over-represented within the islands may both reinforce the methylation blocking and promote transcription. Some histone modifications may also enhance the immunity of the CpG islands against DNA methylation by augmenting these TFs' binding. We speculate that the dynamical equilibrium between methylation spreading and blocking is likely to be responsible for the establishment and maintenance of the relatively stable DNA methylation pattern in human somatic cells.

Highlights

DNA methylation is one of the most important epigenetic modifications
The region between the two ‘0’s on the xaxis represents the U-CpG islands (CGIs) region, the regions outside the two ‘0’s are the flanking regions, and the y-axis is the number of significant Transcription Factor Binding Sites (TFBSs) in each fragment
In [14,35], Brandeis et al and Mummaneni et al reported that Sp1 elements act as a barrier to impede the spreading of DNA methylation, later Sp1 and CTCF elements were observed to be boundary elements to maintain the methylation free state of BRCA1 promoter in normal breast tissue [17]

Summary

Introduction

DNA methylation is one of the most important epigenetic modifications. In mammalian genomes, DNA methylation occurs at the cytosine residue in the context 59-CG-39 (CpG dinucleotide) by virtue of DNA methyltransferases [1]. Some CGIs could be methylated in the imprinted regions [4] or in the inactive X-chromosome [3,11,12], most CGIs are generally resistant to DNA methylation [13] It is still poorly understood what mechanisms may lead to the methylation-resistance of these CGIs. Majority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Our results suggest a possible mechanism that certain putative zinc finger protein binding sites over-represented in the boundary regions of the methylation-resistant CpG islands may block the spreading of methylation into these islands, and those TFBSs over-represented within the islands may both reinforce the methylation blocking and promote transcription. We speculate that the dynamical equilibrium between methylation spreading and blocking is likely to be responsible for the establishment and maintenance of the relatively stable DNA methylation pattern in human somatic cells

Methods

Results

Conclusion