title: 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.
authors.affiliation: Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Tzintzuni I
authors.initials: TI
authors.lastname: Garcia
authors.affiliation: Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany; Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Isa
authors.initials: I
authors.lastname: Matos
authors.affiliation: Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Yingjia
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Vagmita
authors.initials: V
authors.lastname: Pabuwal
authors.affiliation: Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Maria Manuela
authors.initials: MM
authors.lastname: Coelho
authors.affiliation: Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Wakamatsu
authors.affiliation: Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany; Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Schartl
authors.affiliation: Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, Texas State University, San Marcos, Texas, United States of America.
authors.forename: Ronald B
authors.initials: RB
authors.lastname: Walter
mesh_terms: D000483:Alleles; D022981:Allelic Imbalance; D000818:Animals; D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics; D005786:Gene Expression Regulation; D005821:Genetic Techniques; D008969:Molecular Sequence Data; D009990:Oryzias / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D057885:Triploidy
chemical_list: D012333:RNA, Messenger