Cross-species ChIP-seq studies provide insights into regulatory strategies of PPARγ in adipocytes

References

• Siersbæk R, Nielsen R, Mandrup S. Transcriptional networks and chromatin remodeling controlling adipogenesis. Trends Endocrinol Metab 2011; PMID: 22079269
   PubMed Web of Science ®Google Scholar
• Cristancho AG, Lazar MA. Forming functional fat: a growing understanding of adipocyte differentiation. Nat Rev Mol Cell Biol 2011; 12:722 - 34; http://dx.doi.org/10.1038/nrm3198; PMID: 21952300
   PubMed Web of Science ®Google Scholar
• Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, et al. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 2008; 22:2941 - 52; http://dx.doi.org/10.1101/gad.1709008; PMID: 18981473
   PubMed Web of Science ®Google Scholar
• Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, et al. Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 2008; 22:2953 - 67; http://dx.doi.org/10.1101/gad.501108; PMID: 18981474
   PubMed Web of Science ®Google Scholar
• Siersbaek R, Nielsen R, Mandrup S. PPARgamma in adipocyte differentiation and metabolism--novel insights from genome-wide studies. FEBS Lett 2010; 584:3242 - 9; http://dx.doi.org/10.1016/j.febslet.2010.06.010; PMID: 20542036
   PubMed Web of Science ®Google Scholar
• Schmidt SF, Jørgensen M, Chen Y, Nielsen R, Sandelin A, Mandrup S. Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites. BMC Genomics 2011; 12:152; http://dx.doi.org/10.1186/1471-2164-12-152; PMID: 21410980
   PubMed Web of Science ®Google Scholar
• He A, Kong SW, Ma Q, Pu WT. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci U S A 2011; 108:5632 - 7; http://dx.doi.org/10.1073/pnas.1016959108; PMID: 21415370
   PubMed Web of Science ®Google Scholar
• Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008; 133:1106 - 17; http://dx.doi.org/10.1016/j.cell.2008.04.043; PMID: 18555785
   PubMed Web of Science ®Google Scholar
• Siersbæk R, Nielsen R, John S, Sung MH, Baek S, Loft A, et al. Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis. EMBO J 2011; 30:1459 - 72; http://dx.doi.org/10.1038/emboj.2011.65; PMID: 21427703
   PubMed Web of Science ®Google Scholar
• Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, et al. Propagation of adipogenic signals through an epigenomic transition state. Genes Dev 2010; 24:1035 - 44; http://dx.doi.org/10.1101/gad.1907110; PMID: 20478996
   PubMed Web of Science ®Google Scholar
• Boergesen M, Pedersen TA, Gross B, van Heeringen SJ, Hagenbeek D, Bindesbøll C, et al. Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites. Mol Cell Biol 2011; http://dx.doi.org/10.1128/MCB.06175-11; PMID: 22158963
   PubMed Web of Science ®Google Scholar
• Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 2010; 42:631 - 4; http://dx.doi.org/10.1038/ng.600; PMID: 20526341
   PubMed Web of Science ®Google Scholar
• Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 2007; 39:730 - 2; http://dx.doi.org/10.1038/ng2047; PMID: 17529977
   PubMed Web of Science ®Google Scholar
• Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010; 328:1036 - 40; http://dx.doi.org/10.1126/science.1186176; PMID: 20378774
   PubMed Web of Science ®Google Scholar
• Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, et al. Species-specific transcription in mice carrying human chromosome 21. Science 2008; 322:434 - 8; http://dx.doi.org/10.1126/science.1160930; PMID: 18787134
   PubMed Web of Science ®Google Scholar
• Wilson MD, Odom DT. Evolution of transcriptional control in mammals. Curr Opin Genet Dev 2009; 19:579 - 85; http://dx.doi.org/10.1016/j.gde.2009.10.003; PMID: 19913406
   PubMed Web of Science ®Google Scholar
• Johnson R, Samuel J, Ng CK, Jauch R, Stanton LW, Wood IC. Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Mol Biol Evol 2009; 26:1491 - 507; http://dx.doi.org/10.1093/molbev/msp058; PMID: 19318521
   PubMed Web of Science ®Google Scholar
• Dowell RD. Transcription factor binding variation in the evolution of gene regulation. Trends Genet 2010; 26:468 - 75; http://dx.doi.org/10.1016/j.tig.2010.08.005; PMID: 20864205
   PubMed Web of Science ®Google Scholar
• Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010; 143:156 - 69; http://dx.doi.org/10.1016/j.cell.2010.09.006; PMID: 20887899
   PubMed Web of Science ®Google Scholar
• Soccio RE, Tuteja G, Everett LJ, Li Z, Lazar MA, Kaestner KH. Species-specific strategies underlying conserved functions of metabolic transcription factors. Mol Endocrinol 2011; 25:694 - 706; http://dx.doi.org/10.1210/me.2010-0454; PMID: 21292830
   PubMed Web of Science ®Google Scholar
• Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004; 5:276 - 87; http://dx.doi.org/10.1038/nrg1315; PMID: 15131651
   PubMed Web of Science ®Google Scholar
• Hemberg M, Kreiman G. Conservation of transcription factor binding events predicts gene expression across species. Nucleic Acids Res 2011; 39:7092 - 102; http://dx.doi.org/10.1093/nar/gkr404; PMID: 21622661
   PubMed Web of Science ®Google Scholar
• Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009; 462:58 - 64; http://dx.doi.org/10.1038/nature08497; PMID: 19890323
   PubMed Web of Science ®Google Scholar
• Simonis M, Kooren J, de Laat W. An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 2007; 4:895 - 901; http://dx.doi.org/10.1038/nmeth1114; PMID: 17971780
   PubMed Web of Science ®Google Scholar