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Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9. doi: 10.1073/pnas.1413624111. Epub 2014 Nov 20.

Comparison of the transcriptional landscapes between human and mouse tissues.

Author information

1
Department of Genetics, Stanford University, Stanford, CA 94305; Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305;
2
Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110;
3
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
4
Centre for Genomic Regulation and UPF, Catalonia, 08003 Barcelona, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
5
Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742;
6
McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205;
7
Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742; Affymetrix, Inc., Santa Clara, CA 95051; and.
8
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037 ecker@salk.edu mpsnyder@stanford.edu.
9
Department of Genetics, Stanford University, Stanford, CA 94305; ecker@salk.edu mpsnyder@stanford.edu.

Abstract

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.

KEYWORDS:

epigenome; noncoding transcripts; species comparison; transcriptome

PMID:
25413365
PMCID:
PMC4260565
DOI:
10.1073/pnas.1413624111
[Indexed for MEDLINE]
Free PMC Article

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