Abstract
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.
Highlights
Allele specific expression (ASE) is an important component of gene regulation that is not well studied, but is thought to account for a major part of the phenotypic variation within and among species [1,2]
Diploid hybrid nuclei from the developing embryonic blastomeres were transplanted into unfertilized eggs of a third medaka strain
Determination of discriminatory SNPs (dSNPs) To distinguish alleles and determine the contribution of each allele to overall gene expression we focused on using SNPs identified in the three parental strains that had been used to produce the triploids
Summary
Allele specific expression (ASE) is an important component of gene regulation that is not well studied, but is thought to account for a major part of the phenotypic variation within and among species [1,2]. In plants made polyploid through hybridization, homoeologous genes (ancestrally homologous genes incorporated in an allopolyploid organism) can have uneven allele specific expression levels or overall gene expression levels that differ greatly from the parents [4] These homoeologous genes bring together their accompanying regulatory elements which interact with the rest of the regulatory machinery upon hybridization to unevenly affect allele expression and may lead to extensively altered phenotypes [5]. Nondisjunction events result in partially duplicated chromosomes and are mostly incompatible with life in humans, but in other cases lead to large phenotypic disruptions [7]. All of these situations are related to the more basic question of how ASE is affected by the elevation of a diploid genome to a polyploid state
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