RNA-seq analysis of ES cell lines derived from mouse chromosome sibstitution strains

The importance of proper gene regulation to the evolution of reproductive isolation is not well understood. Here we investigated the influence of different subspecies-derived X chromosome on the transcriptional regulation of recipient subspecies genome by using the X-chromosome substitution strain, which shows male-specific sterility. Transcription profiling by microarray experiments showed that large-scale aberrations in gene expression were occurred on the introgressed X chromosome in testes, implying that incompatibilities occurred between cis-regulatory elements of X-linked genes and trans-acting regulatory factors from autosomal genes. Gene ontology analysis showed that meiosis-related genes were preferentially down-regulated. It was reported that vitamin C induces expression of meiosis-related genes in ES cells through the stimulation of the expression of Tet1 gene. To test whether the down-regulation of X-linked genes in the X-chromosome consomic strain was Tet-dependent or not, we performed RNA-seq analysis on ES cell lines derived from wild strains and chromosome substitution strains and compare the expression profiles between strains.