title: Comparison of the transcriptional landscapes between human and mouse tissues.
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.
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305; Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305;
authors.forename: Shin
authors.initials: S
authors.lastname: Lin
authors.affiliation: Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: Yiing
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.affiliation: Centre for Genomic Regulation and UPF, Catalonia, 08003 Barcelona, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
authors.forename: Alessandra
authors.initials: A
authors.lastname: Breschi
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742;
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742;
authors.forename: Alexander
authors.initials: A
authors.lastname: Dobin
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742;
authors.forename: Christopher
authors.initials: C
authors.lastname: Zaleski
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205;
authors.forename: Michael A
authors.initials: MA
authors.lastname: Beer
authors.affiliation: Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110;
authors.forename: William C
authors.initials: WC
authors.lastname: Chapman
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11742; Affymetrix, Inc., Santa Clara, CA 95051; and.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.affiliation: 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.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Department of Genetics, Stanford University, Stanford, CA 94305; ecker@salk.edu mpsnyder@stanford.edu.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Snyder
mesh_terms: D000818:Animals; D021901:DNA, Intergenic / Q000235:genetics*; D057890:Epigenomics / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008810:Mice, Inbred C57BL; D009928:Organ Specificity / Q000235:genetics*; D011506:Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D011506:Proteins
keywords: epigenome; noncoding transcripts; species comparison; transcriptome