Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion

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.

Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa)

“…mexicana was expressed at level about twice as high as the other allele. A previous study on triploid Medaka ( Oryzias latipes ) reported that the maternally inherited allele was never silenced or suppressed, while one paternal allele was completely suppressed in the liver [23]. In cattle, tissue-specific complete suppression of either the maternally or paternally derived allele has been found [22].…”

“…In humans, e.g., up to 60% of the genes show significant ASE differences or allelic bias within and between individuals, populations [17–21], and tissues [22]. About 18% of all examined genes showed uneven expression between alleles in the liver of the triploid Japanese rice fish Oryzias latipes in a large-scale analysis using RNA-seq [23]. This ASE was regulated by either genetic or epigenetic putative allele-specific cis -regulatory factors [24,25].…”

Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish

“…We analyzed the allele expression pattern in four tissues, so in total per gene, approximately 11 (2.7+2.7+2.7+2.7) 'l' allele silencing occurrences should be seen in our evaluation if this phenomenon exists. If AS is not random and affects only a subset of genes or cell types, more genes and other organs need to be investigated in the future, preferably using transcriptomewide approaches as recently described by Garcia et al (2014). (3) AS does not occur at all in the mml genomotypes.…”

“…However, despite new and promising tools that are constantly emerging (Shen et al, 2012a(Shen et al, ,b, 2013, assessing allele-specific gene expression on a large scale is still a technically challenging problem (Garcia et al, 2014), even more so in species with scarce genomic resources, and as in this case, higher levels of ploidy than diploidy. Muscle % 5mC (obs/exp) Liver % 5mC (obs/exp) Fig.…”

“…Hence, allopolyploidy is established 'de novo' at the moment of each individual conception. Another example is the laboratoryproduced TGH allotriploid medakas (Oryzias latipes), where it was found that allele suppression, despite not being abundant, consistently occurred (Garcia et al, 2014).…”