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Autosomal monoallelic expression in the mouse

Lillian M Zwemer1, Alexander Zak25, Benjamin R Thompson2, Andrew Kirby1, Mark J Daly1, Andrew Chess13* and Alexander A Gimelbrant24*

Author Affiliations

1 Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA

2 Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02115, USA

3 Department of Developmental and Regenerative Biology, Fishberg Department of Neuroscience, Department of Genetics and Genomic Sciences, Friedman Brain Institute, Mount Sinai School of Medicine, New York, NY 10029, USA

4 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

5 Current address: Pfizer Research Business Technologies, 35 Cambridgepark Drive, Cambridge, MA 02140, USA

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Genome Biology 2012, 13:R10  doi:10.1186/gb-2012-13-2-r10

Published: 20 February 2012



Random monoallelic expression defines an unusual class of genes displaying random choice for expression between the maternal and paternal alleles. Once established, the allele-specific expression pattern is stably maintained and mitotically inherited. Examples of random monoallelic genes include those found on the X-chromosome and a subset of autosomal genes, which have been most extensively studied in humans. Here, we report a genome-wide analysis of random monoallelic expression in the mouse. We used high density mouse genome polymorphism mapping arrays to assess allele-specific expression in clonal cell lines derived from heterozygous mouse strains.


Over 1,300 autosomal genes were assessed for allele-specific expression, and greater than 10% of them showed random monoallelic expression. When comparing mouse and human, the number of autosomal orthologs demonstrating random monoallelic expression in both organisms was greater than would be expected by chance. Random monoallelic expression on the mouse autosomes is broadly similar to that in human cells: it is widespread throughout the genome, lacks chromosome-wide coordination, and varies between cell types. However, for some mouse genes, there appears to be skewing, in some ways resembling skewed X-inactivation, wherein one allele is more frequently active.


These data suggest that autosomal random monoallelic expression was present at least as far back as the last common ancestor of rodents and primates. Random monoallelic expression can lead to phenotypic variation beyond the phenotypic variation dictated by genotypic variation. Thus, it is important to take into account random monoallelic expression when examining genotype-phenotype correlation.