Gene Expression Divergence between Subspecies of the House Mouse and the Contribution to Reproductive Isolation

Under the Biological Species Concept species are groups of interbreeding individuals that are reproductively isolated from other such groups. A common form of isolation in animals is intrinsic postzygotic isolation via hybrid sterility/inviability. There is a strong consensus that hybrid dysfunctions are caused by epistatic interactions between incompatible alleles from different loci (Dobzhansky-Muller incompatibilities). The identification of genes that contribute to reproductive isolation between taxa is critical to the understanding of the process of speciation, but identifying such genes has proven to be difficult. It appears that regulatory evolution might play an important role in postzygotic isolation and the formation of species. The present study employs a whole genome microarray approach to identify genes with regulatory differences between three subspecies of the house mouse, Mus musculus musculus, M. m. domesticus and M. m. castaneus. The within-locus mode of inheritance for gene expression was assessed for three different tissues (brain, liver and testis) by studying the subspecies and their male reciprocal F1 hybrids. The vast majority of transcripts are additively expressed in the hybrids with only few transcripts showing dominance or overdominance in expression except for one direction of one cross, which shows large misexpression in the testis. The reliability of the observed pattern was ensured by three different analysis methods as well as control experiments. The results suggest that additivity is the general mode of inheritance regarding gene expression changes between house mouse subspecies. Differentially expressed transcripts provide promising candidate genes that could be related to reproductive isolation through regulatory incompatibilities. Several transcripts with expression differences between M. m. musculus and M. m. domesticus were selected for further investigation. A validation approach using quantitative Real-Time PCR strongly emphasizes the need for confirmation of microarray candidate genes. The results show that sequence differences even between closely related taxa have the potential to influence expression data from both microarray and follow-up validation approaches. As divergent gene expression evolution between taxa may be entirely neutral, samples from a transect of the natural musculus-domesticus hybrid zone in Bavaria were analyzed in order to assess functional consequences for two candidate genes. Both genes show large expression differences between the subspecies. The analysis revealed that it is unlikely that the two genes contribute to reproductive isolation between the subspecies as no sign of limited introgression is evident. Rather, the hybrid zone approach in combination with population genetic analyses suggests adaptive introgression of those alleles that are associated with high expression levels. In both cases, the high expression phenotype represents the derived state and is associated with reduced levels of nucleotide polymorphism and a negative Tajima's D. For both genes, regulatory and protein-coding evolution is decoupled and the expression difference results from cis- rather than trans-acting changes

Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes

Microarray analysis reveals that the specific pattern of gene expression in cardiomyocytes derived from embryonic stem cells reflects the biological, physiological and functional processes occurring in mature cardiomyocytes

Gene Expression Disruptions of Organism versus Organ in Drosophila Species Hybrids

Hybrid dysfunctions, such as sterility, may result in part from disruptions in the regulation of gene expression. Studies of hybrids within the Drosophila simulans clade have reported genes expressed above or below the expression observed in their parent species, and such misexpression is associated with male sterility in multigenerational backcross hybrids. However, these studies often examined whole bodies rather than testes or had limited replication using less-sensitive but global techniques. Here, we use a new RNA isolation technique to re-examine hybrid gene expression disruptions in both testes and whole bodies from single Drosophila males by real-time quantitative RT-PCR. We find two early-spermatogenesis transcripts are underexpressed in hybrid whole-bodies but not in assays of testes alone, while two late-spermatogenesis transcripts seem to be underexpressed in both whole-bodies and testes alone. Although the number of transcripts surveyed is limited, these results provide some support for a previous hypothesis that the spermatogenesis pathway in these sterile hybrids may be disrupted sometime after the expression of the early meiotic arrest genes

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Genes of the immune system are generally considered to evolve rapidly due to host–parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated dN/dS ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher dN/dS ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds

A Common and Unstable Copy Number Variant Is Associated with Differences in Glo1 Expression and Anxiety-Like Behavior

Glyoxalase 1 (Glo1) has been implicated in anxiety-like behavior in mice and in multiple psychiatric diseases in humans. We used mouse Affymetrix exon arrays to detect copy number variants (CNV) among inbred mouse strains and thereby identified a ∼475 kb tandem duplication on chromosome 17 that includes Glo1 (30,174,390–30,651,226 Mb; mouse genome build 36). We developed a PCR-based strategy and used it to detect this duplication in 23 of 71 inbred strains tested, and in various outbred and wild-caught mice. Presence of the duplication is associated with a cis-acting expression QTL for Glo1 (LOD>30) in BXD recombinant inbred strains. However, evidence for an eQTL for Glo1 was not obtained when we analyzed single SNPs or 3-SNP haplotypes in a panel of 27 inbred strains. We conclude that association analysis in the inbred strain panel failed to detect an eQTL because the duplication was present on multiple highly divergent haplotypes. Furthermore, we suggest that non-allelic homologous recombination has led to multiple reversions to the non-duplicated state among inbred strains. We show associations between multiple duplication-containing haplotypes, Glo1 expression and anxiety-like behavior in both inbred strain panels and outbred CD-1 mice. Our findings provide a molecular basis for differential expression of Glo1 and further implicate Glo1 in anxiety-like behavior. More broadly, these results identify problems with commonly employed tests for association in inbred strains when CNVs are present. Finally, these data provide an example of biologically significant phenotypic variability in model organisms that can be attributed to CNVs

Widespread Over-Expression of the X Chromosome in Sterile F1 Hybrid Mice

The X chromosome often plays a central role in hybrid male sterility between species, but it is unclear if this reflects underlying regulatory incompatibilities. Here we combine phenotypic data with genome-wide expression data to directly associate aberrant expression patterns with hybrid male sterility between two species of mice. We used a reciprocal cross in which F1 males are sterile in one direction and fertile in the other direction, allowing us to associate expression differences with sterility rather than with other hybrid phenotypes. We found evidence of extensive over-expression of the X chromosome during spermatogenesis in sterile but not in fertile F1 hybrid males. Over-expression was most pronounced in genes that are normally expressed after meiosis, consistent with an X chromosome-wide disruption of expression during the later stages of spermatogenesis. This pattern was not a simple consequence of faster evolutionary divergence on the X chromosome, because X-linked expression was highly conserved between the two species. Thus, transcriptional regulation of the X chromosome during spermatogenesis appears particularly sensitive to evolutionary divergence between species. Overall, these data provide evidence for an underlying regulatory basis to reproductive isolation in house mice and underscore the importance of transcriptional regulation of the X chromosome to the evolution of hybrid male sterility