The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics
Open accessAbstract
Peroxisome proliferator-activated receptor (PPAR) agonists are currently used therapeutically in humans, even though many of their direct gene targets are unknown. Because PPARs can directly regulate gene expression through peroxisome proliferator response elements (PPREs), we pursued the computational prediction of PPREs on a genome-wide scale. Contrary to current hypotheses, PPREs are not isotype-specific, nor do flanking nucleotides confer additional information. However, a position weight matrix-based search for PPREs within upstream conserved elements yielded sufficient selectivity for a genome-wide search. Additionally, a novel motif occurring with greater prevalence than PPREs was revealed. Microarray and gene ontology analyses further validated our search technique and provided new functional clusters of genes that were not previously known to be directly regulated by PPARs (e.g., chromatin remodeling, DNA damage response, Wnt, and mitogen-activated protein kinase signaling). This first genome-wide library of high-confidence predicted PPAR target genes will be a valuable resource to PPAR biologists.
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“The PPAR-RXR dimer binds peroxisome proliferator response elements (PPRE) to activate the transcription of genes within the ATP-binding cassette (ABC) family and genes involved in FA scavenging and lipid metabolism [50,51,76,79].”
From Lipoprotein Lipase Regulates Microglial Lipid Droplet Accumulation (2021) · cites this paper as [50]
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“PPAR agonists have been shown to protect against neuronal death and neuroinflammation, and also to promote CNS repair [50,51].”
From Lipoprotein Lipase Regulates Microglial Lipid Droplet Accumulation (2021) · cites this paper as [50]
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Citations
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
WebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,480
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“These elements, provided via the human Most Conserved track at UCSC, are conserved in space (neighboring nucleotides) and time (human, chimp, mouse, rat, dog, chicken, fugu, and zebrafish genomes), as identified by the phylogenetic hidden Markov model of Siepel et al. ( 16 ).”
BackgroundThe UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,314
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S. E., Scott, G., Steffen, D. L., Worley, K. C., Burch, P. E., et al. (2004) · Nature · doi:10.1038/nature02426 · Cited by 2,170
Hertz, G. Z., & Stormo, G. D. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.7.563 · Cited by 1,246
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
Kel, A. E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg585 · Cited by 1,095
TRANSFAC: a database on transcription factors and their DNA binding sites
Wingender, E. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.238 · Cited by 1,064
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Nissen, S. E., & Wolski, K. (2007) · New England Journal of Medicine · doi:10.1056/nejmoa072761 · Cited by 4,675
Merner, N. D., Hodgkinson, K. A., Haywood, A. F. M., Connors, S. P., French, V. M., Drenckhahn, J., Kupprion, C., Ramadanova, K., Thierfelder, L., McKenna, W. J., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.01.010 · Cited by 528
Chowdhury, P. S., Chamoto, K., Kumar, A., & Honjo, T. (2018) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0095 · Cited by 363
Peroxisome proliferator-activated receptor γ (PPARγ): A master gatekeeper in CNS injury and repair
Cai, W., Yang, T., Liu, H., Han, L., Zhang, K., Hu, X., Zhang, X., Yin, K., Gao, Y., Bennett, M. V. L., et al. (2017) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2017.10.002 · Cited by 240
Martin, M. T., Dix, D. J., Judson, R., Kavlock, R. J., Reif, D. M., Richard, A. M., Rotroff, D. M., Romanov, S., Medvedev, A. V., Poltoratskaya, N., et al. (2010) · Chemical Research in Toxicology · doi:10.1021/tx900325g · Cited by 217
Metadata
- Authors
- Lemay, D. G., & Hwang, D. H.
- Affiliations
- Agricultural Research Service (US)
- Venue
- Journal of Lipid Research
- Publisher
- Elsevier BV
- Published
- 2006-07
- Volume
- 47
- Issue
- 7
- Pages
- 1583-1587
- ISSN
- 0022-2275 (ISSN-L)
- OpenAlex
- W2147427406
- Cited by
- 143
- References
- 21
- Citations by year
- 2026: 1 · 2025: 3 · 2023: 2 · 2022: 3 · 2021: 6 · 2020: 3 · 2019: 5 · 2018: 12 · 2017: 4 · 2016: 4 · 2015: 6 · 2014: 8 · 2013: 11 · 2012: 14
- FWCI
- 5.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Lipid Research (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Agriculture (01A095Rev)
- National Institutes of Health
- Agricultural Research Service
- National Institute of Diabetes and Digestive and Kidney Diseases (DK-064007, R01DK064007)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Peroxisome Proliferator-Activated Receptors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Nutrition, Genetics, and Disease
- Keywords
- peroxisome proliferator response element, peroxisome proliferator-activated receptors, PPAR target genes, transcription factor binding site prediction, position weight matrices, PPAR agonists, chromatin remodeling, DNA damage response, Wnt signaling, MAPK signaling
- MeSH terms
- Animals, DNA, Gene Expression Regulation, Humans, Gene Library, Genome, Human, Conserved Sequence, Computational Biology, Oligonucleotide Array Sequence Analysis, Genomics, Peroxisome Proliferator-Activated Receptors, Mice, Rats
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