Stochastic Choice of Allelic Expression in Human Neural Stem Cells

Abstract

Monoallelic gene expression, such as genomic imprinting, is well described. Less well‐characterized are genes undergoing stochastic monoallelic expression (MA), where specific clones of cells express just one allele at a given locus. We performed genome‐wide allelic expression assessment of human clonal neural stem cells derived from cerebral cortex, striatum, and spinal cord, each with differing genotypes. We assayed three separate clonal lines from each donor, distinguishing stochastic MA from genotypic effects. Roughly 2% of genes showed evidence for autosomal MA, and in about half of these, allelic expression was stochastic between different clones. Many of these loci were known neurodevelopmental genes, such as OTX2 and OLIG2. Monoallelic genes also showed increased levels of DNA methylation compared to hypomethylated biallelic loci. Identified monoallelic gene loci showed altered chromatin signatures in fetal brain, suggesting an in vivo correlate of this phenomenon. We conclude that stochastic allelic expression is prevalent in neural stem cells, providing clonal diversity to developing tissues such as the human brain. Stem Cells2012;30:1938–1947

Erasure and reestablishment of random allelic expression imbalance after epigenetic reprogramming

“…Autosomal genes can also undergo random monoallelic expression, with initial descriptions of its occurrence in immune genes (Mostoslavsky et al 2001) and the olfactory receptors (Chess et al 1994), providing cellular diversity within these systems. Recent high-throughput allelic expression profiling of human clonal lymphoblastoid, fibroblast, and neural stem cells has shown that stochastic allelic expression is more prevalent than previously thought, affecting up to 10% of autosomal expressed transcripts across a diverse range of cell types (Gimelbrant et al 2007;Chess 2012;Jeffries et al 2012;Li et al 2012;Zwemer et al 2012). This process has also been observed in mouse, with a significant overlap in loci characterized by random monoallelic expression across species (Zwemer et al 2012).…”

“…Approximately 7000 autosomal genes contained informative (heterozygous) transcribed SNPs (see Materials and Methods) allowing us to make quantitative allelic expression measurements. Based on previous allelic expression studies (Pastinen et al 2004;Serre et al 2008;Lee et al 2009;Jeffries et al 2012) and Xchromosome inactivation profiles (Supplemental Fig. S2), we categorized the expression of genes as biallelic (BA), allelically skewed, and monoallelic (MA) according to the degree of allelic bias detected.…”

“…Many of these NSC1 and NSC2 genes represent novel MA loci and were not characterized by MA expression in the original SPC01 line. The limited gene ontology analyses we could undertake given the small number of input loci provided evidence for an overrepresentation of proteins integral to the plasma membrane (GO:0005887, P = 0.04, 1.97-fold enrichment), reflecting the patterns seen in the original clonal neural stem cell before reprogramming in addition to neural stem cells from other brain regions (Jeffries et al 2012) and clonal lymphoblastoid cells (Gimelbrant et al 2007).…”

“…It has been shown that while biallelic genes are synchronously replicated in S-phase, random monoallelically expressed genes show asynchronous replication, even before the activation of transcription (Kitsberg et al 1993;Simon et al 1999). Epigenetic processes such as DNA methylation and histone modifications are also associated with this form of transcriptional control (Jeffries et al 2012;Nag et al 2013). While increased DNA methylation at the gene promoter is associated with monoallelic gene expression (Gendrel et al 2014), DNA methylation on its own may not be sufficient for allelic expression control (Eckersley-Maslin et al 2014;Gendrel et al 2014).…”

“…Stochastic monoallelic loci are distributed across the genome and encompass most functional gene ontologies, although some studies indicate that they are enriched among cell surface molecules (Gimelbrant et al 2007;Jeffries et al 2012). Two recent studies examined the developmental patterns of random monoallelic expression using clonally expanded embryonic stem cells (ES) and neural progenitor cells from outcrossed mice (Eckersley-Maslin et al 2014;Gendrel et al 2014).…”