Monoallelic Expression of Multiple Genes in the CNS

Abstract

The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F1 (C57BL/6×JF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.

Random monoallelic expression: regulating gene expression one allele at a time

“…These approaches assume the active and inactive alleles are marked by different epigenetic features, such as DNA methylation [31,32] or histone modifications [30]. As these data-sets are derived from non-clonal cell populations to identify monoallelically expressed genes such analysis comes with several caveats.…”

“…This is distinct from classic monoallelically expressed genes such as imprinted genes, olfactory receptors and protocadherins (Table 2). Furthermore, there is a lack of chromosome coordination of random monoallelically expressed genes [22,23,31]: that is, genes in the same genomic region will not necessarily be expressed from the same allele. Secondly, the genes exhibiting random monoallelic expression encode proteins of a wide-range of functions.…”

“…Simultaneous DNA methylation and lack of DNA methylation was used to identify potential monoallelically expressed genes in the mouse CNS [31,32], of which ~12% were confirmed to be monoallelically expressed in clonal cell populations [32]. The remaining genes likely reflect false positives due to the heterogeneous mix of cell types used in the original assay.…”

Monoallelic Expression Determines Oncogenic Progression and Outcome in Benign and Malignant Brain Tumors

“…For most other genes, expression is typically expected to occur from both parental alleles without preference. Recent studies, however, have uncovered a potential role for random MAE, as well as differential allele-specific expression (DAE; i.e., a skew in allelespecific expression rather than complete monoallelic expression) in normal tissues as well as in some diseases, including cancer (3)(4)(5)(6)(7)(8)(9).…”

Epigenetic Manifestations in Diet-Related Disorders

“…This is referred to as mono-allelic expression. Of course, one could start from the genomic methylation profile to select potential candidate genes and test them for monoallelic expression [57] . In a more direct approach, Gimelbrant et al [58] analyzed RNA as cDNA on the Affymetrix 500 K SNP array and compared the signals with those from genomic, bi-allelic DNA.…”