TY  - JOUR
A1  - Garcia, Tzintzuni I.
A1  - Matos, Isa
A1  - Shen, Yingjia
A1  - Pabuwal, Vagmita
A1  - Coelho, Maria Manuela
A1  - Wakamatsu, Yuko
A1  - Schartl, Manfred
A1  - Walter, Ronald B.
T1  - Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
T2  - PLOS ONE
N2  - 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.
KW  - RNA-SEQ data
KW  - copy-number alteration
KW  - squalius alburnoides
KW  - gene expression
KW  - medaka
KW  - variant detection
KW  - transplantation
KW  - genome
KW  - generation
KW  - evolution
Y1  - 2014
UR  - https://opus.bibliothek.uni-wuerzburg.de/frontdoor/index/index/docId/11600
UR  - https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-116000
SN  - 1932-6203
VL  - 9
IS  - 6
ER  -