An encyclopedia of mouse DNA elements (Mouse ENCODE)
Open accessAbstract
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.
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In mice, PP2A expression was detected in all thirty adult or embryonic tissues examined by RNA-seq, with highest expression in brain and lowest in adult liver.
“In mice, PP2A expression was found in all of thirty adult or embryonic tissues examined by RNA-seq through the Mouse ENCODE Initiative, overall showing the highest expression in brain, and the lowest in adult liver (Fig. 2) [19].”
From Physiologic functions of PP2A: Lessons from genetically modified mice (2019) · cites this paper as [19]
Most B-type subunits appear ubiquitously expressed, but some are restricted to specific tissues and likely mediate tissue-specific PP2A functions.
“While the large majority of B-type subunits appear ubiquitously expressed, some of them are restricted to specific tissues, and therefore, likely mediate tissue-specific PP2A functions (Fig. 2).”
From Physiologic functions of PP2A: Lessons from genetically modified mice (2019) · cites this paper as [19]
Some PP2A genes are developmentally regulated: B55β and B55γ expression increases during embryonic brain development, while SET, ANP32A, ANP32E and CIP2A expression decreases during brain and liver development.
“Finally, some PP2A genes appear developmentally regulated, best illustrated for B55β and B55γ, the expression of which increases during embryonic brain development, while expression of the PP2A inhibitors SET, ANP32A, ANP32E and CIP2A, conversely, decreases during brain development, and also during liver development (Fig. 2).”
From Physiologic functions of PP2A: Lessons from genetically modified mice (2019) · cites this paper as [19]
A SNP in the Oxtr 3' untranslated region, NT204321, had a minor allele frequency of 33% in the prairie vole colony.
“One SNP in the 3’ untranslated region (minor allele frequency 33%), heretofore referred to as NT204321 based on the position of this nucleotide on a sequenced prairie vole bacterial artificial clone (58) (DP001215.2), was identified using this method.”
From Variation in the Oxytocin Receptor Gene Predicts Brain Region–Specific Expression and Social Attachment (2016) · cites this paper as [58]
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Cites
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works
Self-citationInitial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works
Self-citationThe ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390 · see citing works
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
The ENCODE Project Consortium (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001046 · Cited by 1,495 · see citing works
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · see citing works
Self-citationA high-resolution map of human evolutionary constraint using 29 mammals
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108 · see citing works
Self-citationChromatin accessibility pre-determines glucocorticoid receptor binding patterns
John, S., Sabo, P. J., Thurman, R. E., Sung, M.-H., Biddie, S. C., Johnson, T. A., Hager, G. L., & Stamatoyannopoulos, J. A. (2011) · Nature Genetics · doi:10.1038/ng.759 · Cited by 954 · see citing works
Self-citationAnimal models of diabetes mellitus
Rees, A., & Alcolado, J. C. (2005) · Diabetic Medicine · doi:10.1111/j.1464-5491.2005.01499.x · Cited by 735 · see citing works
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559 · see citing works
Self-citationDeletion of Ultraconserved Elements Yields Viable Mice
Ahituv, N., Zhu, Y., Visel, A., Holt, A., Afzal, V., Pennacchio, L. A., & Rubin, E. M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050234 · Cited by 319 · see citing works
Mouse models of human disease. Part II: recent progress and future directions.Preprint
Bedell, M. A., Largaespada, D. A., Jenkins, N. A., & Copeland, N. G. (1997) · Genes & Development · doi:10.1101/gad.11.1.11 · Cited by 193 · see citing works
ENCODE whole-genome data in the UCSC genome browser (2011 update)
Raney, B. J., Cline, M., Rosenbloom, K. R., Dreszer, T. R., Learned, K., Barber, G. P., Meyer, L. R., Sloan, C. A., Malladi, V. S., Roskin, K. M., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1017 · Cited by 178 · see citing works
Self-citationMiller, W., Makova, K. D., Nekrutenko, A., & Hardison, R. C. (2004) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.5.061903.180057 · Cited by 163 · see citing works
Self-citationGenome-scale analysis of replication timing: from bench to bioinformatics
Ryba, T., Battaglia, D., Pope, B. D., Hiratani, I., & Gilbert, D. M. (2011) · Nature Protocols · doi:10.1038/nprot.2011.328 · Cited by 131 · see citing works
Self-citationFunctional autonomy of distant-acting human enhancers
Visel, A., Akiyama, J. A., Shoukry, M. I., Afzal, V., Rubin, E. M., & Pennacchio, L. A. (2009) · Genomics · doi:10.1016/j.ygeno.2009.02.002 · Cited by 63 · see citing works
Mouse models for human disease
Hardouin, S., & Nagy, A. (2000) · Clinical Genetics · doi:10.1034/j.1399-0004.2000.570401.x · Cited by 59 · see citing works
Determining Spatial Chromatin Organization of Large Genomic Regions Using 5C Technology
van Berkum, N. L., & Dekker, J. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-414-2_13 · Cited by 46 · see citing works
Self-citationComparative Genomics for Detecting Human Disease Genes
Moreno, C., Lazar, J., Jacob, H. J., & Kwitek, A. E. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00423-3 · Cited by 23 · see citing works
Hoit, B. D. (2001) · Trends in Cardiovascular Medicine · doi:10.1016/s1050-1738(01)00090-1 · Cited by 19 · see citing works
Limits of sequence and functional conservation
Pennacchio, L. A., & Visel, A. (2010) · Nature Genetics · doi:10.1038/ng0710-557 · Cited by 17 · see citing works
Cheng, J., Priest, J. R., & Pennacchio, L. A. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-030-0_13 · Cited by 5 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- ENCODE Data Coordination Center at UCSC [http://www.encodeproject.org/ENCODE/terms.html] doi:10.1186/gb-2012-13-8-418 Cite this article as: Stamatoyannopoulos JA, et al.: An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology 2012, 13:418.
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Ji, Y., Zhou, Z., Liu, H., & Davuluri, R. V. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab083 · Cited by 1,303 · see citing works
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Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works
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Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944 · see citing works
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Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794 · see citing works
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Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1168 · Cited by 670 · see citing works
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Self-citation
- Authors
- Mouse ENCODE Consortium, Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., Canfield, T., Giste, E., Johnson, A., Zhang, M., Balasundaram, G., Byron, R., Roach, V., Sabo, P. J., Sandstrom, R., Stehling, A. S., Thurman, R. E., Weissman, S. M., Cayting, P., Hariharan, M., Lian, J., Cheng, Y., Landt, S. G., Ma, Z., Wold, B. J., Dekker, J., Crawford, G. E., Keller, C. A., Wu, W., Morrissey, C., Kumar, S. A., Mishra, T., Jain, D., Byrska-Bishop, M., Blankenberg, D., Lajoie, B. R., Jain, G., Sanyal, A., Chen, K.-B., Denas, O., Taylor, J., Blobel, G. A., Weiss, M. J., Pimkin, M., Deng, W., Marinov, G. K., Williams, B. A., Fisher-Aylor, K. I., Desalvo, G., Kiralusha, A., Trout, D., Amrhein, H., Mortazavi, A., Edsall, L., McCleary, D., Kuan, S., Shen, Y., Yue, F., Ye, Z., Davis, C. A., Zaleski, C., Jha, S., Xue, C., Dobin, A., Lin, W., Fastuca, M., Wang, H., Guigo, R., Djebali, S., Lagarde, J., Ryba, T., Sasaki, T., Malladi, V. S., Cline, M. S., Kirkup, V. M., Learned, K., Rosenbloom, K. R., Kent, W. J., Feingold, E. A., Good, P. J., Pazin, M., Lowdon, R. F., & Adams, L. B.
- Affiliations
- University of Washington (US)
- Stanford Medicine (US)
- Pennsylvania State University (US)
- University of California San Diego (US)
- Cold Spring Harbor Laboratory (US)
- Florida State University (US)
- Fred Hutch Cancer Center (US)
- Yale University (US)
- California Institute of Technology (US)
- University of Massachusetts Chan Medical School (US)
- Duke University (US)
- Emory University (US)
- Children's Hospital of Philadelphia (US)
- University of California, Irvine (US)
- Centre for Genomic Regulation (ES)
- University of California, Santa Cruz (US)
- National Institutes of Health (US)
- Corresponding author
- Stamatoyannopoulos, John A
- ORCID
- Stamatoyannopoulos, John A
- Snyder, Michael
- Hardison, Ross
- Ren, Bing
- Gingeras, Thomas
- Gilbert, David M
- Groudine, Mark
- Kaul, Rajinder
- Balasundaram, Gayathri
- Sabo, Peter J
- Sandstrom, Richard
- Hariharan, Manoj
- Cheng, Yong
- Wold, Barbara J
- Dekker, Job
- Crawford, Gregory E
- Keller, Cheryl A
- Mishra, Tejaswini
- Jain, Deepti
- Blankenberg, Daniel
- Lajoie, Bryan R
- Jain, Gaurav
- Sanyal, Amartya
- Taylor, James
- Blobel, Gerd A
- Weiss, Mitchell J
- Deng, Wulan
- Marinov, Georgi K
- Williams, Brian A
- Fisher-Aylor, Katherine I
- Desalvo, Gilberto
- Trout, Diane
- Amrhein, Henry
- Mortazavi, Ali
- Edsall, Lee
- Kuan, Samantha
- Yue, Feng
- Ye, Zhen
- Lin, Wei
- Djebali, Sarah
- Lagarde, Julien
- Ryba, Tyrone
- Sasaki, Takayo
- Malladi, Venkat S
- Cline, Melissa S
- Learned, Katrina
- Rosenbloom, Kate R
- Pazin, Michael
- Lowdon, Rebecca F
- Adams, Leslie B
- Venue
- Genome Biology
- Published
- 2012-08-13
- Volume
- 13
- Issue
- 8
- Pages
- 418-418
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC3491367
- OpenAlex
- W2039176012
- Cited by
- 446
- References
- 22
- Citations by year
- 2026: 1 · 2025: 11 · 2024: 23 · 2023: 17 · 2022: 17 · 2021: 29 · 2020: 28 · 2019: 27 · 2018: 36 · 2017: 43 · 2016: 48 · 2015: 50 · 2014: 64 · 2013: 44 · 2012: 7
- FWCI
- 21.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- The Journal of the American Medical Association (JAMA) Network (American Medical Association) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- Funders
- Yale University
- Children's Hospital of Philadelphia
- Emory University
- California Institute of Technology
- National Institutes of Health
- University of California, Irvine
- National Human Genome Research Institute (RC2HG005573, R01HG003143)
- National Institute of General Medical Sciences (T32GM081739, P01GM085354)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK065806, R37DK044746)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- DNA elements, functional genomic annotation, mouse genomics, ENCODE, regulatory elements
- MeSH terms
- Animals, Humans, Genome, Human, Genome, Internet, Genomics, Databases, Nucleic Acid, Mice, Molecular Sequence Annotation
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