Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

Abstract

CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity Purification plus deep sequencing (CAP-seq). We also asked whether CGIs not associated with annotated transcripts share properties with those at known promoters. We found that, contrary to previous estimates, CGI abundance in humans and mice is very similar and many are at conserved locations relative to genes. In each species CpG density correlates positively with the degree of H3K4 trimethylation, supporting the hypothesis that these two properties are mechanistically interdependent. Approximately half of mammalian CGIs (>10,000) are “orphans” that are not associated with annotated promoters. Many orphan CGIs show evidence of transcriptional initiation and dynamic expression during development. Unlike CGIs at known promoters, orphan CGIs are frequently subject to DNA methylation during development, and this is accompanied by loss of their active promoter features. In colorectal tumors, however, orphan CGIs are not preferentially methylated, suggesting that cancer does not recapitulate a developmental program. Human and mouse genomes have similar numbers of CGIs, over half of which are remote from known promoters. Orphan CGIs nevertheless have the characteristics of functional promoters, though they are much more likely than promoter CGIs to become methylated during development and hence lose these properties. The data indicate that orphan CGIs correspond to previously undetected promoters whose transcriptional activity may play a functional role during development.

Distinct p53 genomic binding patterns in normal and cancer-derived human cells

“…Proximal CGIs (close to TSSs) typically are hypomethylated, while distal CGIs (far from TSSs, also known as "orphans") are more likely to be methylated in normal somatic cells. 63 Most p53 ChIP-seq peaks are in proximal although some are in distal CGIs (Figs. 6D and S9).…”

Cell type–specific DNA methylation at intragenic CpG islands in the immune system

“…This is true for both TSS and intragenic CGIs, although the proportion of intragenic CGIs marked by H3K4me3 is smaller, with 41% of intragenic CGIs positive for H3K4me3 in embryonic stem (ES) cells compared to 96% of TSS CGIs . Methylated CGIs, on the other hand, do not associate with H3K4me3, reflecting transcriptional silencing at these sites (Meissner et al 2008;Illingworth et al 2010;Maunakea et al 2010). Recent studies have suggested a mechanistic explanation for this phenomenon whereby the protein CFP1 binds to unmethylated CGIs and facilitates recruitment of the SET1 H3K4 methyltransferase complex (Thomson et al 2010).…”

Aberrant methylation of the GCK gene body is associated with the risk of essential hypertension

“…Gene-body methylation identified 'orphan promoters', which may be used in the early stages of development (30). Hypermethylation of gene-bodies frequently indicates higher levels of gene expression in human tissues and cell types (8,31).…”