DNA methylation is a key mechanism for maintaining monoallelic expression on autosomes

Abstract

Thousands of mammalian genes show epigenetically controlled unequal transcription of the parental alleles. Genes subject to autosomal monoallelic expression (MAE) display mitotically stable allelic choice, leading to persistent transcriptional differences between clonal cell lineages. Mechanism of MAE mitotic maintenance is unknown. Using a new screening-by-sequencing strategy, we uncovered a key role for DNA methylation in MAE maintenance. Subset of MAE loci were insensitive to DNA demethylation, suggesting mechanistic heterogeneity of MAE. Genome-wide analyses indicate that MAE is part of a more general mode of gene regulation and reveal a previously unappreciated interplay of genetic and epigenetic control of allele-specific transcription. While cis-acting regulation defines a common underlying state for all cells, DNA methylation plays the role of an allele-specific rheostat and determines multiple regulatory states distinguishing between developmentally equivalent clonal cell lineages. Our findings imply that allele-specific analyses of clonal cell populations can unmask longterm transcriptional responses to drug-driven perturbations.

DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

“…5d,e). Furthermore, NRG1 and PCDH7 are mono-allelically expressed genes and DLC1 was recently reported to be partially mono-allelically expressed (Gupta et al, 2020). Interesting, we found that loss of allelic replication for these three genes specifically involved loss of the early replicating allele in DKO1.…”

“…In agreement, loss of allelic replication at key cancer-related genes (TP53 and RB1) was found in cancer patient lymphocytes treated with the demethylation agent 5-azacytidine (Dotan et al, 2004(Dotan et al, , 2008Nagler et al, 2010). There is also evidence for DNA methylation involvement in non-imprinted monoallelic expression in both humans (da Rocha and Gendrel, 2019; Schalkwyk et al, 2010) and mice (Gupta et al, 2020). We further identified that loss of allelic replication was associated with expression down-regulation at three colon cancer-related gene loci that are also monoallelically expressed.…”

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

“…Monoallelic expression is reported to differ in frequency between grades of brain tumors (Walker et al, 2012) and in colorectal tumors compared to normal tissue (Liu et al, 2018), suggesting that cancer cells can acquire ectopic allele-specific expression during transformation. DNA methylation is also involved in non-imprinted monoallelic expression in both humans and mice (da Rocha and Gendrel, 2019;Gupta et al, 2020;Schalkwyk et al, 2010). We found that the majority of allele-specific replicating loci lost their allelic replication after DNA hypomethylation, suggesting that DNA methylation may also play a role in the regulation of allelically replicating genes that are also monoallelically expressed.…”

“…Notably, three genes that lose allelic replication in DKO1 cells are also reported to be associated with colon cancer: NRG1 (Luraghi et al, 2017;Stahler et al, 2017), PCDH7 (Li et al, 2020;van Roy, 2014), and DLC1 (Durkin et al, 2007;Peng et al, 2013) (Figures 5C, 5D, S6D, and S6E). NRG1 and PCDH7 are also mono-allelically Article ll expressed genes, and DLC1 was recently reported to be partially mono-allelically expressed (Gupta et al, 2020). All three genes are significantly downregulated in DKO1 compared to HCT116 (Figure S6J); interestingly, they show loss of the early replicating allele in DKO1 (Figures 5D and S6E).…”

Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system

“…RNA-seq data analysis followed the same pipeline as for HSC derived clones in vivo, with exception of the maternal reference genome which was 129S1. These data were originally generated for the work described in bioRxiv by Gupta et al, 2020 Preprint 52 .…”