Pruning of the Adipocyte Peroxisome Proliferator-Activated Receptor γ Cistrome by Hematopoietic Master Regulator PU.1

REFERENCES

• Cherry AB, Daley GQ. 2012. Reprogramming cellular identity for regenerative medicine. Cell 148:1110–1122.
   PubMed Web of Science ®Google Scholar
• Bussmann LH, Schubert A, Vu Manh TP, De Andres L, Desbordes SC, Parra M, Zimmermann T, Rapino F, Rodriguez-Ubreva J, Ballestar E, Graf T. 2009. A robust and highly efficient immune cell reprogramming system. Cell. Stem Cell 5:554–566.
   PubMedGoogle Scholar
• Ladewig J, Koch P, Brustle O. 2013. Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies. Nat. Rev. Mol. Cell Biol. 14:225–236.
   Web of Science ®Google Scholar
• Margariti A, Winkler B, Karamariti E, Zampetaki A, Tsai TN, Baban D, Ragoussis J, Huang Y, Han JD, Zeng L, Hu Y, Xu Q. 2012. Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels. Proc. Natl. Acad. Sci. U. S. A. 109:13793–13798.
   PubMed Web of Science ®Google Scholar
• Islas JF, Liu Y, Weng KC, Robertson MJ, Zhang S, Prejusa A, Harger J, Tikhomirova D, Chopra M, Iyer D, Mercola M, Oshima RG, Willerson JT, Potaman VN, Schwartz RJ. 2012. Transcription factors ETS2 and MESP1 transdifferentiate human dermal fibroblasts into cardiac progenitors. Proc. Natl. Acad. Sci. U. S. A. 109:13016–13021.
   PubMed Web of Science ®Google Scholar
• Huang P, He Z, Ji S, Sun H, Xiang D, Liu C, Hu Y, Wang X, Hui L. 2011. Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors. Nature 475:386–389.
   PubMed Web of Science ®Google Scholar
• Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. 2008. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature 455:627–632.
   PubMed Web of Science ®Google Scholar
• Yanger K, Zong Y, Maggs LR, Shapira SN, Maddipati R, Aiello NM, Thung SN, Wells RG, Greenbaum LE, Stanger BZ. 2013. Robust cellular reprogramming occurs spontaneously during liver regeneration. Genes Dev. 27:719–724.
   PubMed Web of Science ®Google Scholar
• Heinz S, Glass CK. 2012. Roles of lineage-determining transcription factors in establishing open chromatin: lessons from high-throughput studies. Curr. Top. Microbiol. Immunol. 356:1–15.
   PubMedGoogle Scholar
• Zaret KS, Carroll JS. 2011. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25:2227–2241.
   PubMed Web of Science ®Google Scholar
• Lefterova MI, Steger DJ, Zhuo D, Qatanani M, Mullican SE, Tuteja G, Manduchi E, Grant GR, Lazar MA. 2010. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol. Cell. Biol. 30:2078–2089.
   PubMed Web of Science ®Google Scholar
• Scott EW, Simon MC, Anastasi J, Singh H. 1994. Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages. Science 265:1573–1577.
   PubMed Web of Science ®Google Scholar
• DeKoter RP, Singh H. 2000. Regulation of B lymphocyte and macrophage development by graded expression of PU.1. Science 288:1439–1441.
   PubMed Web of Science ®Google Scholar
• Feng R, Desbordes SC, Xie H, Tillo ES, Pixley F, Stanley ER, Graf T. 2008. PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells. Proc. Natl. Acad. Sci. U. S. A. 105:6057–6062.
   PubMed Web of Science ®Google Scholar
• Forsberg M, Carlen M, Meletis K, Yeung MS, Barnabe-Heider F, Persson MA, Aarum J, Frisen J. 2010. Efficient reprogramming of adult neural stem cells to monocytes by ectopic expression of a single gene. Proc. Natl. Acad. Sci. U. S. A. 107:14657–14661.
   PubMed Web of Science ®Google Scholar
• Laiosa CV, Stadtfeld M, Xie H, de Andres-Aguayo L, Graf T. 2006. Reprogramming of committed T cell progenitors to macrophages and dendritic cells by C/EBP alpha and PU.1 transcription factors. Immunity 25:731–744.
   PubMed Web of Science ®Google Scholar
• Xie H, Ye M, Feng R, Graf T. 2004. Stepwise reprogramming of B cells into macrophages. Cell 117:663–676.
   PubMed Web of Science ®Google Scholar
• Tontonoz P, Spiegelman BM. 2008. Fat and beyond: the diverse biology of PPARgamma. Annu. Rev. Biochem. 77:289–312.
   PubMed Web of Science ®Google Scholar
• Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJJr, Liu XS, Lazar MA. 2008. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev. 22:2941–2952.
   PubMed Web of Science ®Google Scholar
• MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ. 2011. Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet. 27:141–148.
   PubMedGoogle Scholar
• Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, Denissov S, Borgesen M, Francoijs KJ, Mandrup S, Stunnenberg HG. 2008. 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. 22:2953–2967.
   PubMed Web of Science ®Google Scholar
• Waki H, Nakamura M, Yamauchi T, Wakabayashi K, Yu J, Hirose-Yotsuya L, Take K, Sun W, Iwabu M, Okada-Iwabu M, Fujita T, Aoyama T, Tsutsumi S, Ueki K, Kodama T, Sakai J, Aburatani H, Kadowaki T. 2011. Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genet. 7:e1002311. doi:10.1371/journal.pgen.1002311.
   PubMedGoogle Scholar
• Tontonoz P, Nagy L, Alvarez JG, Thomazy VA, Evans RM. 1998. PPARgamma promotes monocyte/macrophage differentiation and uptake of oxidized LDL. Cell 93:241–252.
   PubMed Web of Science ®Google Scholar
• Chen Z, Vigueira PA, Chambers KT, Hall AM, Mitra MS, Qi N, McDonald WG, Colca JR, Kletzien RF, Finck BN. 2012. Insulin resistance and metabolic derangements in obese mice are ameliorated by a novel peroxisome proliferator-activated receptor gamma-sparing thiazolidinedione. J. Biol. Chem. 287:23537–23548.
   PubMed Web of Science ®Google Scholar
• Kanda T, Brown JD, Orasanu G, Vogel S, Gonzalez FJ, Sartoretto J, Michel T, Plutzky J. 2009. PPARgamma in the endothelium regulates metabolic responses to high-fat diet in mice. J. Clin. Invest. 119:110–124.
   PubMedGoogle Scholar
• Lu M, Sarruf DA, Talukdar S, Sharma S, Li P, Bandyopadhyay G, Nalbandian S, Fan W, Gayen JR, Mahata SK, Webster NJ, Schwartz MW, Olefsky JM. 2011. Brain PPAR-gamma promotes obesity and is required for the insulin-sensitizing effect of thiazolidinediones. Nat. Med. 17:618–622.
   PubMed Web of Science ®Google Scholar
• Cipolletta D, Feuerer M, Li A, Kamei N, Lee J, Shoelson SE, Benoist C, Mathis D. 2012. PPAR-gamma is a major driver of the accumulation and phenotype of adipose tissue Treg cells. Nature 486:549–553.
   PubMed Web of Science ®Google Scholar
• Chawla A, Barak Y, Nagy L, Liao D, Tontonoz P, Evans RM. 2001. PPAR-gamma dependent and independent effects on macrophage-gene expression in lipid metabolism and inflammation. Nat. Med. 7:48–52.
   PubMed Web of Science ®Google Scholar
• Ricote M, Li AC, Willson TM, Kelly CJ, Glass CK. 1998. The peroxisome proliferator-activated receptor-gamma is a negative regulator of macrophage activation. Nature 391:79–82.
   PubMed Web of Science ®Google Scholar
• Nagy L, Tontonoz P, Alvarez JG, Chen H, Evans RM. 1998. Oxidized LDL regulates macrophage gene expression through ligand activation of PPARgamma. Cell 93:229–240.
   PubMed Web of Science ®Google Scholar
• Roszer T, Menendez-Gutierrez MP, Lefterova MI, Alameda D, Nunez V, Lazar MA, Fischer T, Ricote M. 2011. Autoimmune kidney disease and impaired engulfment of apoptotic cells in mice with macrophage peroxisome proliferator-activated receptor gamma or retinoid X receptor alpha deficiency. J. Immunol. 186:621–631.
   PubMedGoogle Scholar
• Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38:576–589.
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat. Biotechnol. 29:24–26.
   PubMed Web of Science ®Google Scholar
• Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. 2008. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26:1293–1300.
   PubMed Web of Science ®Google Scholar
• Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12:R83–2011-12-8-r83. doi:10.1186/gb-2011-12-8-r83.
   PubMedGoogle Scholar
• McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28:495–501.
   PubMed Web of Science ®Google Scholar
• Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS. 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481:389–393.
   PubMed Web of Science ®Google Scholar
• Tusher VG, Tibshirani R, Chu G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U. S. A. 98:5116–5121.
   PubMed Web of Science ®Google Scholar
• Schupp M, Cristancho AG, Lefterova MI, Hanniman EA, Briggs ER, Steger DJ, Qatanani M, Curtin JC, Schug J, Ochsner SA, McKenna NJ, Lazar MA. 2009. Re-expression of GATA2 cooperates with peroxisome proliferator-activated receptor-gamma depletion to revert the adipocyte phenotype. J. Biol. Chem. 284:9458–9464.
   PubMed Web of Science ®Google Scholar
• Tontonoz P, Graves RA, Budavari AI, Erdjument-Bromage H, Lui M, Hu E, Tempst P, Spiegelman BM. 1994. Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha. Nucleic Acids Res. 22:5628–5634.
   PubMed Web of Science ®Google Scholar
• Siersbæk R, Nielsen R, John S, Sung MH, Baek S, Loft A, Hager GL, Mandrup S. 2011. Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis. EMBO J. 30:1459–1472.
   PubMed Web of Science ®Google Scholar
• Schmidt SF, Jorgensen M, Chen Y, Nielsen R, Sandelin A, Mandrup S. 2011. Cross species comparison of C/EBPalpha and PPARgamma profiles in mouse and human adipocytes reveals interdependent retention of binding sites. BMC Genomics 12:152–2164-12-152. doi:10.1186/1471-2164-12-152.
   PubMed Web of Science ®Google Scholar
• Lattin JE, Schroder K, Su AI, Walker JR, Zhang J, Wiltshire T, Saijo K, Glass CK, Hume DA, Kellie S, Sweet MJ. 2008. Expression analysis of G protein-coupled receptors in mouse macrophages. Immunome Res. 4:5–7580-4-5. doi:10.1186/1745-7580-4-5.
   PubMedGoogle Scholar
• Graf T, Enver T. 2009. Forcing cells to change lineages. Nature 462:587–594.
   PubMed Web of Science ®Google Scholar
• Ieda M, Fu JD, Delgado-Olguin P, Vedantham V, Hayashi Y, Bruneau BG, Srivastava D. 2010. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142:375–386.
   PubMed Web of Science ®Google Scholar
• Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Langst G, Benner C, Rehli M. 2013. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. [Epub ahead of print.] doi:10.1093/nar/gkt355.
   Google Scholar
• Caramel J, Medjkane S, Quignon F, Delattre O. 2008. The requirement for SNF5/INI1 in adipocyte differentiation highlights new features of malignant rhabdoid tumors. Oncogene 27:2035–2044.
   PubMedGoogle Scholar
• Debril MB, Gelman L, Fayard E, Annicotte JS, Rocchi S, Auwerx J. 2004. Transcription factors and nuclear receptors interact with the SWI/SNF complex through the BAF60c subunit. J. Biol. Chem. 279:16677–16686.
   PubMedGoogle Scholar
• Lin L, Pang W, Chen K, Wang F, Gengler J, Sun Y, Tong Q. 2012. Adipocyte expression of PU.1 transcription factor causes insulin resistance through upregulation of inflammatory cytokine gene expression and ROS production. Am. J. Physiol. Endocrinol. Metab. 302:E1550–E1559.
   PubMedGoogle Scholar
• Bugge A, Mandrup S.31 August 2010, posting date.Molecular mechanisms and genome-wide aspects of PPAR subtype specific transactivation. PPAR Res. 2010:169506. doi:10.1155/2010/169506.
   PubMedGoogle Scholar
• Gupta P, Gurudutta GU, Saluja D, Tripathi RP. 2009. PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis. J. Cell. Mol. Med. 13:4349–4363.
   PubMed Web of Science ®Google Scholar
• Meyer ME, Gronemeyer H, Turcotte B, Bocquel MT, Tasset D, Chambon P. 1989. Steroid hormone receptors compete for factors that mediate their enhancer function. Cell 57:433–442.
   PubMed Web of Science ®Google Scholar
• Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. 2006. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38:1289–1297.
   PubMed Web of Science ®Google Scholar
• He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. 2012. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 22:1015–1025.
   PubMed Web of Science ®Google Scholar