title: A comparative encyclopedia of DNA elements in the mouse genome.
abstract: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.
authors.affiliation: 1] Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania 17033, USA.
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authors.lastname: Guigo
authors.affiliation: Functional Genomics, Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.affiliation: Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, Florida 32306-4295, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Gilbert
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine and Department of Biomedical Engineering, Johns Hopkins University, 733 N. Broadway, BRB 573 Baltimore, Maryland 21205, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Beer
authors.affiliation: Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Ren
mesh_terms: D000818:Animals; D019070:Cell Lineage / Q000235:genetics; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D003850:Deoxyribonuclease I / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D016678:Genome / Q000235:genetics*; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D051379:Mice / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012313:RNA / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D002843:Chromatin; D014157:Transcription Factors; D012313:RNA; D003850:Deoxyribonuclease I