A comparative encyclopedia of DNA elements in the mouse genome.

TitleA comparative encyclopedia of DNA elements in the mouse genome.
Publication TypeJournal Article
Year of Publication2014
AuthorsYue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD et al.
Corporate AuthorsMouse ENCODE Consortium
JournalNature
Volume515
Issue7527
Pagination355-64
Date Published2014 Nov 20
ISSN1476-4687
KeywordsAnimals, Cell Lineage, Chromatin, Conserved Sequence, Deoxyribonuclease I, DNA Replication, Gene Expression Regulation, Gene Regulatory Networks, Genome, Genome-Wide Association Study, Genomics, Humans, Mice, Molecular Sequence Annotation, Regulatory Sequences, Nucleic Acid, RNA, Species Specificity, Transcription Factors, Transcriptome
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.

DOI10.1038/nature13992
Alternate JournalNature
PubMed ID25409824
PubMed Central IDPMC4266106
Grant ListF31 CA165863 / CA / NCI NIH HHS / United States
U01 HL099656 / HL / NHLBI NIH HHS / United States
R01 HG007175 / HG / NHGRI NIH HHS / United States
MC_UU_12009/2 / MRC_ / Medical Research Council / United Kingdom
P01 GM085354 / GM / NIGMS NIH HHS / United States
P30 CA008748 / CA / NCI NIH HHS / United States
R01 HG007348 / HG / NHGRI NIH HHS / United States
U01 HG004695 / HG / NHGRI NIH HHS / United States
U54 HG007004 / HG / NHGRI NIH HHS / United States
F32 HL110473 / HL / NHLBI NIH HHS / United States
R01 HG004037 / HG / NHGRI NIH HHS / United States
R01 DK096266 / DK / NIDDK NIH HHS / United States
RC2 HG005573 / HG / NHGRI NIH HHS / United States
K99 HG007356 / HG / NHGRI NIH HHS / United States
R01HD043997-09 / HD / NICHD NIH HHS / United States
R56 DK065806 / DK / NIDDK NIH HHS / United States
F32HL110473 / HL / NHLBI NIH HHS / United States
1U54HG007004 / HG / NHGRI NIH HHS / United States
R01 HD043997 / HD / NICHD NIH HHS / United States
3RC2HG005602 / HG / NHGRI NIH HHS / United States
F31CA165863 / CA / NCI NIH HHS / United States
K99 HL119617 / HL / NHLBI NIH HHS / United States
R01HG003991 / HG / NHGRI NIH HHS / United States
P01 HL064190 / HL / NHLBI NIH HHS / United States
GM085354 / GM / NIGMS NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States
R37 DK044746 / DK / NIDDK NIH HHS / United States
R01 DK065806 / DK / NIDDK NIH HHS / United States
RC2HG005573 / HG / NHGRI NIH HHS / United States
P30 CA045508 / CA / NCI NIH HHS / United States
R01 ES024992 / ES / NIEHS NIH HHS / United States
T32 GM081739 / GM / NIGMS NIH HHS / United States
/ WT_ / Wellcome Trust / United Kingdom
U01 HL099993 / HL / NHLBI NIH HHS / United States
R01DK065806 / DK / NIDDK NIH HHS / United States
P01 HL110860 / HL / NHLBI NIH HHS / United States
U54 HG006997 / HG / NHGRI NIH HHS / United States
R01 GM083337 / GM / NIGMS NIH HHS / United States
R01 HG003991 / HG / NHGRI NIH HHS / United States
GM083337 / GM / NIGMS NIH HHS / United States
RC2 HG005602 / HG / NHGRI NIH HHS / United States
R01 EY021482 / EY / NEI NIH HHS / United States
R01 HG007354 / HG / NHGRI NIH HHS / United States
U54 HG006998 / HG / NHGRI NIH HHS / United States
095908 / WT_ / Wellcome Trust / United Kingdom
K99HL119617 / HL / NHLBI NIH HHS / United States
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