Journal Article

Comparison of the transcriptional landscapes between human and mouse tissues

Chapman, William C., Lin, Shin, Lin, Yiing, Nery, Joseph R., Breschi, Alessandra, Dobin, Alexander, Snyder, Michael P., Ecker, Joseph R., Zaleski, Christopher, Davis, Carrie A., Beer, Michael A., Urich, Mark A., Gingeras, Thomas R.

2014

Overview

Significance To date, various studies have found similarities between humans and mice on a molecular level, and indeed, the murine model serves as an important experimental system for biomedical science. In this study of a broad number of tissues between humans and mice, high-throughput sequencing assays on the transcriptome and epigenome reveal that, in general, differences dominate similarities between the two species. These findings provide the basis for understanding the differences in phenotypes and responses to conditions in humans and mice. Although the similarities between humans and mice are typically highlighted, morphologically and genetically, there are many differences. To better understand these two species on a molecular level, we performed a comparison of the expression profiles of 15 tissues by deep RNA sequencing and examined the similarities and differences in the transcriptome for both protein-coding and -noncoding transcripts. Although commonalities are evident in the expression of tissue-specific genes between the two species, the expression for many sets of genes was found to be more similar in different tissues within the same species than between species. These findings were further corroborated by associated epigenetic histone mark analyses. We also find that many noncoding transcripts are expressed at a low level and are not detectable at appreciable levels across individuals. Moreover, the majority lack obvious sequence homologs between species, even when we restrict our attention to those which are most highly reproducible across biological replicates. Overall, our results indicate that there is considerable RNA expression diversity between humans and mice, well beyond what was described previously, likely reflecting the fundamental physiological differences between these two organisms.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: animal models / Animals / Biological Sciences / biomedical research / Comparative analysis / Datasets / Disease models / DNA, Intergenic - genetics / Epigenetics / Epigenomics - methods / Evolution, Molecular / Gene expression / Gene Expression Profiling - methods / Genes / Genomes / High-Throughput Nucleotide Sequencing / Histones / Humans / landscapes / Mice / Mice, Inbred C57BL / Organ Specificity - genetics / phenotype / Principal components analysis / Proteins / Proteins - genetics / Ribonucleic acid / RNA / Rodents / Sequence Analysis, RNA / Species / Species Specificity / Tissue samples / Tissues / transcription (genetics) / transcriptome / Transcriptome - genetics