Wang, Xu2012-12-172016-12-302011-08-31bibid: 7955564https://hdl.handle.net/1813/30738Genomic imprinting is a special form of epigenetic modification of the genome in which gene expression differs in an allele-specific manner depending on the parent-oforigin. The degree of imprinting is often tissue- and/or developmental stage-specific, and may be altered in some diseases including cancer. To date, 99 genes have been shown to undergo genomic imprinting in mouse, and 60 are imprinted in humans, with an overlapping set of 43 imprinted in both species. This list is far from complete, and obtaining an exhaustive identification of imprinted genes would expand our understanding of the regulation and evolution of the phenomenon. To search for novel imprinted genes, I applied custom SNP microarray and Illumina mRNA sequencing technologies to the transcriptomes of reciprocal F1 mouse brains and placentas. In brain, I identified 26 genes with parent-of-origin dependent differential allelic expression. Pyrosequencing verified 17 of them, including three novel imprinted genes. In placenta, I confirmed the imprinting status of 23 known imprinted genes, and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in placenta. Through a well-replicated design using an orthogonal allelicexpression technology, I verified five novel imprinted genes that were not previously known to be imprinted in mouse. After repeated application to multiple tissues and developmental stages this approach will yield a complete catalog of imprinted genes, shedding light on the mechanism and evolution of imprinted genes and diseases associated with genomic imprinting. X-inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues. After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, I applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains, and found a small but consistent and highly statistically significant tendency to under-express the paternal X chromosome. Allelic bias in expression is also influenced by the sampling effect of X inactivation and by cis-acting regulatory variation, and for each gene we quantified the contributions of these effects in two different strain combinations while controlling for variability in Xce alleles.en-USGenomic imprintingX chromosome inactivationreciprocal crossdissertation or thesis