Contrasting chromatin organization of CpG islands and exons in the human genome

Abstract

Background: CpG islands and nucleosome-free regions are both found in promoters. However, their association has never been studied. On the other hand, DNA methylation is absent in promoters but is enriched in gene bodies. Intragenic nucleosomes and their modifications have been recently associated with RNA splicing. Because the function of intragenic DNA methylation remains unclear, I explored the possibility of its involvement in splicing regulation.

Results: Here I show that CpG islands were associated not only with methylation-free promoters but also with nucleosome-free promoters. Nucleosome-free regions were observed only in promoters containing a CpG island. However, the DNA sequences of CpG islands predicted the opposite pattern, implying a limitation of sequence programs for the determination of nucleosome occupancy. In contrast to the methylation-and nucleosome-free states of CpG-island promoters, exons were densely methylated at CpGs and packaged into nucleosomes. Exon-enrichment of DNA methylation was specifically found in spliced exons and in exons with weak splice sites. The enrichment patterns were less pronounced in initial exons and in non-coding exons, potentially reflecting a lower need for their splicing. I also found that nucleosomes, DNA methylation, and H3K36me3 marked the exons of transcripts with low, medium, and high gene expression levels, respectively.

Conclusions: Human promoters containing a CpG island tend to remain nucleosome-free as well as methylation-free. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. Exonic DNA methylation seems to function together with exonic nucleosomes and H3K36me3 for the proper splicing of transcripts with different expression levels.

Figure 1

Nucleosome organization of promoter CGIs. (a-c) Nucleosome patterns upstream, inside and downstream of the CGI (from left to right) based on (a) in vivo nucleosome occupancy for human T cells [5] measured as normalized read count (NRC; see Materials and methods), (b) sequence prediction of nucleosome occupancy [15], and (c) DNA bending propensity. (d,e) Nucleosome patterns surrounding the transcription start site (TSS) based on (d) in vivo nucleosome occupancy for human T cells [5] measured as the NRC and (e) sequence prediction of nucleosome occupancy [15].

Figure 2

Exonic DNA methylation and nucleosome occupancy. (a) Nucleosome occupancy (upper panel) and CpG methylation (lower panel) plotted as the average of all transcripts across non-coding exons (NCEs), coding exons, and flanking introns according to their relative positions within the transcript. All exons and introns were partitioned into ten bins and the average normalized read count (NRC) was obtained for each bin of all corresponding exons and introns. ICEs (initial coding exons) and LCEs (last coding exons) are broken into the UTR (light blue or light green) and coding region (dark blue or dark green) by the start codon and stop codon, respectively. The ends of the introns (orange) are connected to those of the flanking exons by the black lines. (b) Exon inclusiveness measured as the relative expression of each internal exon compared to the other exons in the transcript. The lowest 10% were considered spliced out and the others to be spliced in. The top 10% were identified as highly expressed for the purpose of checking for sequencing bias. (c) Comparison of nucleosome occupancy (upper panel) and CpG methylation (lower panel) among skipped exons, included exons, and highly expressed exons as defined above. tss, transcriptions start site.

Figure 3

Normalized nucleosome occupancy, CpG methylation, and H3K36me3 density. (a,b) Normalized nucleosome occupancy, CpG methylation, and H3K36me3 density for internal exons versus (a) the quantiles of gene expression level and (b) pol II elongation efficiency. The gray lines indicate the percentage of CGI promoters within each bin (y-axis on the right-hand side).