Hyperconserved CpG domains underlie Polycomb-binding sites

Abstract

Comparative genomics of CpG dinucleotides, which are targets of DNA methyltransferases in vertebrate genomes, has been constrained by their evolutionary instability and by the effect of methylation on their mutation rates. We compared the human and chimpanzee genomes to identify DNA sequence signatures correlated with rates of mutation at CpG dinucleotides. The new signatures were used to develop robust comparative genomics of CpG dinucleotides in heterogeneous regions and to identify genomic domains that have anomalous CpG divergence rates. The data showed that there are Ϸ200 genomic regions where CpG distributions are far more conserved than predicted. These hyperconserved CpG domains largely coincide with domains bound by Polycomb repressive complex 2 in undifferentiated human embryonic stem cells and are almost exclusively present near genes whose products are involved in the regulation of embryonic development. Several domains were experimentally shown to be unmethylated at different developmental stages. These data indicate that particular evolutionary patterns and distinct sequence properties on scales much larger than standard transcription factor-binding sites may play an important role in Polycomb recruitment and transcriptional regulation of key developmental genes.comparative genomics ͉ development ͉ DNA methylation ͉ epigenetics ͉ evolution O xidative deamination of 5-methylcytosine (m 5 C) converts the base to thymine, and most m 5 CpG dinucleotides in vertebrate genomes are rapidly (1, 2) mutated to TpG or CpA. For example, Ͼ20% of the CpGs have diverged in the otherwise 99.2% identical human and chimp genomes. Unmethylated CpG dinucleotides are mutated at normal rates, and regions with low levels of methylation, such as CpG islands (3, 4), have consequently higher CpG contents than regions with high levels of methylation. Conservation of CpG dinucleotides may therefore be a consequence of low germ-line methylation or of purifying selection against the loss of functional CpGs. Here we show that the sequence context of a CpG can be used to accurately model its divergence rate, in accordance with recent evidence on the correlation between sequence context and methylation levels (5-7). Our model predicts that CpG divergence rates vary by a factor of 40 as a function of sequence context and show that context-aware models are essential for the analysis of CpG evolution in heterogeneous regions.We suggest that comparative genomics offer insights into longstanding questions as to the function of DNA methylation. We demonstrate this by identifying genomic regions in which CpGs are far more conserved than expected. These hyperconserved CpG domains (HCGDs) we identify show extensive overlap with regions bound by Polycomb repressive complex 2 (PRC2) and are observed almost exclusively at genes related to the regulation of embryonic development.

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

“…Because the majority of SUZ12 peaks lie within CGIs (20,21), we asked if candidate CGIs can act autonomously to promote H3K27me3 when inserted in a heterologous genomic environment. We Significance Polycomb repressive complex 2 functions in gene repression and acts by methylating histone H3 at lysine 27 (H3K27me3).…”

“…S4G), indicating that CpG dinucleotides are required for H3K27me3 recruitment. Such a model has previously been proposed based on the strong presence of H3K27me3 at CGIs (20,21) and the observation that two CpG-rich elements from the Escherichia coli genome become H3K27-methylated when placed into stem cells as part of larger transgenes (22,23). The identification of small endogenous sequences that can autonomously recruit H3K27me3 enabled us to rigorously test this model.…”

“…Several transcription factor (TF) binding motifs are enriched within fly PREs and might contribute to Polycomb recruitment (18,19). In mammals, PRC2 and the H3K27me3 mark localize mainly to transcriptionally inactive regions rich in CpG dinucleotides, referred to as CpG-islands (CGIs) (20)(21)(22)(23). CGIs are unique to vertebrate genomes that show global DNA methylation (24).…”

Genomic regulatory blocks underlie extensive microsynteny conservation in insects

“…In vertebrates, Polycomb group proteins are also preferentially found at the loci of developmental regulatory genes Lee et al 2006), were shown to bind to evolutionarily conserved CpG islands that overlap large portions of developmental regulatory genes (Tanay et al 2007), and directly control CpG methylation (Vire et al 2006). Even though insects do not have genome methylation or CpG islands, one can speculate that Polycomb binding regions in Drosophila are functionally equivalent to conserved CpG islands in mammals.…”

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

“…In contrast, the Polycomb group protein EZH2 has been shown to interact with both DNMT1 and DNMT3 to deliver DNA methylation at the sites of its recruitment (Vire et al 2006). Surprisingly, studies carried out in different models demonstrated that DNA methylation and H3K27me3 probably take part in different regulatory pathways as they usually mark different gene populations (Tanay et al 2007;Fouse et al 2008;Komashko et al 2008;Kondo et al 2008;Rush et al 2009). DNA methylation is not essential for pluripotency as ES cells can proliferate but not differentiate in the absence of DNMT1 (Chen et al 2003;Jackson et al 2004;Tsumura et al 2006).…”