Genetic and Epigenetic Regulation of Pvt1 Monoallelic Expression

Each gene exists as two copies in the same nucleus of mammalian cells. Although most genes are equivalently controlled on both alleles, Random Monoallelic Expressing (RME) genes stably maintain the expression from only one of two alleles, but the mechanisms and functional consequences of RME remains unclear. Here we performed allele-specific RNA-seq on over 100 neural progenitor cell (NPC) clonal lines to reveal the extent of RME for genes across clonal lines. Interestingly out of 297 autosomal RME genes, Pvt1, a well-studied oncogenic long non-coding RNA, is monoallelically expressed with a skewed genetic bias towards the Castaneous allele in F1-hybrid NPCs. In the absence of genetic differences, allelic tracking by gene editing reveals Pvt1 undergoes balanced RME that is maintained across somatic cell generations. Monoallelic expression is maintained by a poised Pvt1 promoter with bivalent active histone marks, H3K4me3 and H3K27ac, and silencing histone marks, H3K4me3 and H3K27me3, demonstrating its ability to switch transcriptional states depending on the cellular context. Leveraging our large RNA-seq data set and the genetic skew, we use differential gene expression analysis on clonal lines based on their Pvt1 allelic status to reveal a transcription factor, Tfap2a, with differential binding at the Pvt1 promoter, providing a mechanism for the initiation and allelic choice for RME genes. Additionally, we demonstrate monoallelic Pvt1 expression results in an increase in Pvt1 expression leading to a growth advantage relative to Pvt1 biallelic expressing clonal lines These findings provide an example of how genetic differences can skew a stochastic process which results in an epigenetic phenomenon with a phenotypic consequence in early development.