Mechanism of monoallelic expression and allelic rheostat role of DNA methylation (RRBS)

In mammalian cells, large groups of genes show epigenetically controlled unequal transcription of maternal and paternal alleles. Thousands of autosomal genes subject to monoallelic expression (MAE) comprise the largest such group. The initial random allelic choice in these loci is followed by mitotically stable transmission of the allele-specific state, leading to stable epigenetic and functional differences between clonal cell lineages. Molecular mechanisms underpinning MAE maintenance are not known. We devised and performed a drug screen for reactivation of epigenetically silenced alleles in mouse cells, using a new strategy based on deep targeted allele-specific RNA sequencing, which can read out multiple loci simultaneously. We found that, contrary to previous observations, DNA methylation plays a key role in mitotic memory of MAE in multiple autosomal loci. Having established that a specific perturbation can affect multiple loci, we assessed genome-wide impact of the drug exposure in several clonal cell lines, identifying over 600 genes with allele-specific expression changing with DNA methylation. We found that multiple distinct states of allele-specific expression correspond to the extent of DNA methylation and can be stably maintained, indicating allelic rheostat role of DNA methylation. Our findings reveal a previously unappreciated interplay of genetic and epigenetic control of allele-specific expression and reinforce the role of such regulation in maintaining differences between developmentally equivalent clonal cell lineages. RRBS was performed in immortalised B cell line, Abl.1 clonal cell line of 129xCastF1 background [1,2] before and after treatment with 5-aza-2'-deoxycytidine (5-aza-dC). Libraries (minimum 2 replicates per sample, except otherwise mentioned) were sequenced and data was analyzed. [1] Zwemer, L.M., Zak, A., Thompson, B.R., Kirby, A., Daly, M.J., Chess, A., and Gimelbrant, A.A. (2012). Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10. [2] Nag, A., Savova, V., Fung, H.-L., Miron, A., Yuan, G.-C., Zhang, K., Gimelbrant, A.A., and Gingeras, T. (2013). Chromatin signature of widespread monoallelic expression. eLife 2, e01256.