Monoallelic Gene Expression in Health and Disease

Although most genes in the genome of diploid organisms are expressed from both alleles, genes in some tissues are transcribed preferentially from a single allele. Sex chromosome gene dosage compensation is the first described and best known example of such monoallelic expression. In order to balance expression of X-linked genes, which are present in two copies in females, the majority of one of the X-chromosome genes are transcriptionally silenced in a process called X-chromosome inactivation; however, it has subsequently been shown that monoallelic expression also occurs in some autosomal genes. Genomic imprinting, another example of monoallelic expression, is characterized by transcription in a parent-of-origin-dependent manner. There is clinical relevance of imprinting since a parenteral location of the same genetic lesion may be associated with disorders of entirely different phenotypes. Yet another mechanism of preferential allele usage is allelic exclusion, which occurs in specialized cell types (e.g., B-lymphocytes express only a single heavy and light chain and each olfactory neuron expresses a single odorant receptor gene from greater than 1,300 genes). In the examples given above, allele-specific transcription is not fully understood but may be attained by one or a combination of mechanisms, including asymmetric DNA methylation, replication timing, chromatin structure, non-coding RNAs, and nuclear localization.

Two recent papers have contributed to the elucidation and significance of the mechanism by which two homologous alleles will be targeted for inactivation in so-called random monoallelic expression. Alexander and colleagues employed mouse embryonic stem cell lines that have yet to choose the allele for inactivation and used fluorescence in situ hybridization probes targeted to specific genes. These investigators could then detect and differentiate between the active and inactive states of specific loci during the S-phase by the presence of a single fluorescent pinpoint in replicated loci that was characteristic of the active state, while a doublet on the homologous chromosome indicated its tendency for inactivation. In their paper, Alexander, et al. noted that alleles subjected to monoallelic expression on both autosomes and X-chromosomes often flipped between the active and inactive states in the embryonic stem cells. The inability to assay the state of activity of monoallelic loci in methanol fixed cells suggested a requirement for intact chromatin structure. Based on this, the authors investigated whether embryonic stem cells carrying mutations in either Eed or Dnmt1, proteins that are known to play a role in chromatin modification, would affect the allelic inactivation, and their results showed a pivotal role for Eed gene in the establishment of the active/inactive state.

A second paper by Scholl and colleagues unveiled a pivotal role for the clustered homeobox (HOX) genes in normal hematopoiesis and observed their abnormal expression in the majority of patients with acute myeloid leukemia (AML). A normal human genome carries 39 HOX transcription factors clustered on four chromosomes (HOXA - 7p15, HOXB - 17q21, HOXC - 12q12, and HOXD - 2q31); expression of the genes within each cluster is developmentally, temporally, and spatially correlated to their location within each loci. Gene expression from these loci is under complex transcriptional and epigenetic regulation. One family of transcription factors, the Caudal-like homeobox genes (CDX1, CDX2, and CDX4), plays a critical role in regulating expression of HOX genes. Normal expression of CDX2 is restricted to intestinal development in the adult, while aberrant expression has been linked to gastrointestinal malignancies. The authors of this report first showed that the ectopic expression of CDX2 in a mouse was sufficient to induce malignant leukemic transformation. In their study of human AML, they showed that 153 of 170 patients (90 percent) and eight of 15 human myeloid leukemia cell lines (53 percent) expressed CDX2 regardless of their cytogenetic status. These investigators then studied the mechanism of aberrant CDX2 expression and discovered that six of seven patients expressed CDX2 from a single allele. However, the molecular basis of this monoallelic expression of CDX2 remains unclear as no mutations in the promoter, its exons, or hypomethylation of CpG island of CDX2 exon-1 were found.