Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid
biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial
polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (
trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in
polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a
biological model system we have used nuclear
transplantation to experimentally produce artificial
triploid medaka composed of three different haplomes. We measured ASE in
RNA isolated from the livers of two adult,
triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both
triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both
triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both
triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.