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Analysis of Enhancers and Transcriptional Networks in Thermogenic Adipocytes

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Brown Adipose Tissue

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2448))

Abstract

Transcription factor (TF) networks orchestrate the regulation of gene programs in mammalian cells, including white and brown adipocytes. In this protocol, we outline how genomics and transcriptomics data can be integrated to infer causal TFs of a given cellular response or cell type using “Integrated analysis of Motif Activity and Gene Expression changes of transcription factors” (IMAGE). Here, we show how key regulatory TFs controlling white and brown adipocyte gene programs can be predicted from chromatin accessibility and RNA-seq data. Furthermore, we demonstrate how information about target sites and target genes of the predicted key regulators can be integrated to propose testable hypotheses regarding the role and mechanisms of TFs.

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References

  1. Kim SH, Plutzky J (2016) Brown fat and browning for the treatment of obesity and related metabolic disorders. Diabetes Metab J 40(1):12–21. https://doi.org/10.4093/dmj.2016.40.1.12

    Article  PubMed  PubMed Central  Google Scholar 

  2. Levy SE, Myers RM (2016) Advancements in next-generation sequencing. Annu Rev Genomics Hum Genet 17:95–115. https://doi.org/10.1146/annurev-genom-083115-022413

    Article  CAS  PubMed  Google Scholar 

  3. Loft A, Forss I, Mandrup S (2017) Genome-wide insights into the development and function of thermogenic adipocytes. Trends Endocrinol Metab 28(2):104–120. https://doi.org/10.1016/j.tem.2016.11.005

    Article  CAS  PubMed  Google Scholar 

  4. Stark R, Grzelak M, Hadfield J (2019) RNA sequencing: the teenage years. Nat Rev Genet 20(11):631–656. https://doi.org/10.1038/s41576-019-0150-2

    Article  CAS  PubMed  Google Scholar 

  5. Gao T, Qian J (2020) EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic Acids Res 48(D1):D58–D64. https://doi.org/10.1093/nar/gkz980

    Article  CAS  PubMed  Google Scholar 

  6. Pang B, Snyder MP (2020) Systematic identification of silencers in human cells. Nat Genet 52(3):254–263. https://doi.org/10.1038/s41588-020-0578-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132(2):311–322. https://doi.org/10.1016/j.cell.2007.12.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16(1):123–131. https://doi.org/10.1101/gr.4074106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6(4):283–289. https://doi.org/10.1038/nmeth.1313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res 17(6):877–885. https://doi.org/10.1101/gr.5533506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10(12):1213–1218. https://doi.org/10.1038/nmeth.2688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA (2012) The accessible chromatin landscape of the human genome. Nature 489(7414):75–82. https://doi.org/10.1038/nature11232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Yan F, Powell DR, Curtis DJ, Wong NC (2020) From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis. Genome Biol 21(1):22. https://doi.org/10.1186/s13059-020-1929-3

    Article  PubMed  PubMed Central  Google Scholar 

  14. Buenrostro JD, Wu B, Chang HY, Greenleaf WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109:21.29.1–21.29.9. https://doi.org/10.1002/0471142727.mb2129s109

  15. Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Rottger R, Baumbach J, Scheele C, Kassem M, Mandrup S (2019) Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet 51(4):716–727. https://doi.org/10.1038/s41588-019-0359-1

  16. Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14(10):959–962. https://doi.org/10.1038/nmeth.4396

  17. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523(7561):486–490. https://doi.org/10.1038/nature14590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459(7243):108–112. https://doi.org/10.1038/nature07829

  19. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467(7314):430–435. https://doi.org/10.1038/nature09380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 33(11):1165–1172. https://doi.org/10.1038/nbt.3383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Cejas P, Li L, O'Neill NK, Duarte M, Rao P, Bowden M, Zhou CW, Mendiola M, Burgos E, Feliu J, Moreno-Rubio J, Guadalajara H, Moreno V, Garcia-Olmo D, Bellmunt J, Mullane S, Hirsch M, Sweeney CJ, Richardson A, Liu XS, Brown M, Shivdasani RA, Long HW (2016) Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nat Med 22(6):685–691. https://doi.org/10.1038/nm.4085

    Article  CAS  PubMed  Google Scholar 

  22. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Muller F, Forrest ARR, Carninci P, Rehli M, Sandelin A (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455–461. https://doi.org/10.1038/nature12787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182–187. https://doi.org/10.1038/nature09033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322(5909):1845–1848. https://doi.org/10.1126/science.1162228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kwak H, Fuda NJ, Core LJ, Lis JT (2013) Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339(6122):950–953. https://doi.org/10.1126/science.1229386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 31(13):3576–3579. https://doi.org/10.1093/nar/gkg585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. 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(4):576–589. https://doi.org/10.1016/j.molcel.2010.05.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK (2011) Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 21(3):447–455. https://doi.org/10.1101/gr.112623.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK (2014) Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 32(2):171–178. https://doi.org/10.1038/nbt.2798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5(4):276–287. https://doi.org/10.1038/nrg1315

    Article  CAS  PubMed  Google Scholar 

  31. Schmidt SF, Madsen JG, Frafjord KO, Poulsen L, Salo S, Boergesen M, Loft A, Larsen BD, Madsen MS, Holst JJ, Maechler P, Dalgaard LT, Mandrup S (2016) Integrative genomics outlines a biphasic glucose response and a ChREBP-RORgamma axis regulating proliferation in beta cells. Cell Rep 16(9):2359–2372. https://doi.org/10.1016/j.celrep.2016.07.063

    Article  CAS  PubMed  Google Scholar 

  32. Consortium F, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Riken Omics Science C, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 41(5):553–562. https://doi.org/10.1038/ng.375

    Article  CAS  Google Scholar 

  33. Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E (2014) ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 24(5):869–884. https://doi.org/10.1101/gr.169508.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Madsen JGS, Rauch A, Van Hauwaert EL, Schmidt SF, Winnefeld M, Mandrup S (2018) Integrated analysis of motif activity and gene expression changes of transcription factors. Genome Res 28(2):243–255. https://doi.org/10.1101/gr.227231.117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Siersbaek MS, Loft A, Aagaard MM, Nielsen R, Schmidt SF, Petrovic N, Nedergaard J, Mandrup S (2012) Genome-wide profiling of peroxisome proliferator-activated receptor gamma in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression. Mol Cell Biol 32(17):3452–3463. https://doi.org/10.1128/MCB.00526-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Loft A, Forss I, Siersbaek MS, Schmidt SF, Larsen AS, Madsen JG, Pisani DF, Nielsen R, Aagaard MM, Mathison A, Neville MJ, Urrutia R, Karpe F, Amri EZ, Mandrup S (2015) Browning of human adipocytes requires KLF11 and reprogramming of PPARgamma superenhancers. Genes Dev 29(1):7–22. https://doi.org/10.1101/gad.250829.114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Siersbaek 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(8):1459–1472. https://doi.org/10.1038/emboj.2011.65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7:3. https://doi.org/10.1186/1471-2199-7-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE, Stamatoyannopoulos JA (2013) Genome-scale mapping of DNase I hypersensitivity. Curr Protoc Mol Biol, Chapter 27:Unit 21.27. https://doi.org/10.1002/0471142727.mb2127s103

  40. Nielsen R, Mandrup S (2014) Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq. Methods Enzymol 537:261–279. https://doi.org/10.1016/B978-0-12-411619-1.00014-8

    Article  CAS  PubMed  Google Scholar 

  41. Dobin A, Gingeras TR (2016) Optimizing RNA-Seq mapping with STAR. Methods Mol Biol 1415:245–262. https://doi.org/10.1007/978-1-4939-3572-7_13

    Article  CAS  PubMed  Google Scholar 

  42. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635

    Article  CAS  PubMed  Google Scholar 

  43. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. https://doi.org/10.1093/bioinformatics/btp324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Madsen JG, Schmidt SF, Larsen BD, Loft A, Nielsen R, Mandrup S (2015) iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic Acids Res 43(6):e40. https://doi.org/10.1093/nar/gku1365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Shapira SN, Lim HW, Rajakumari S, Sakers AP, Ishibashi J, Harms MJ, Won KJ, Seale P (2017) EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex. Genes Dev 31(7):660–673. https://doi.org/10.1101/gad.294405.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Zhang H, Huang Y, Lee HJ, Jin W (2015) Zic1 negatively regulates brown adipogenesis in C3H10T1/2 cells. Sci Bull 60(11):1033–1035. https://doi.org/10.1007/s11434-015-0797-9

    Article  CAS  Google Scholar 

  47. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. https://doi.org/10.1093/bioinformatics/btp616

    Article  CAS  PubMed  Google Scholar 

  48. Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS (2017) Cistrome data browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res 45(D1):D658–D662. https://doi.org/10.1093/nar/gkw983

    Article  CAS  PubMed  Google Scholar 

  49. Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR (2018) GIGGLE: a search engine for large-scale integrated genome analysis. Nat Methods 15(2):123–126. https://doi.org/10.1038/nmeth.4556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Loft A, Alfaro AJ, Schmidt SF, Pedersen FB, Terkelsen MK, Puglia M, Chow KK, Feuchtinger A, Troullinaki M, Maida A, Wolff G, Sakurai M, Berutti R, Ekim Ustunel B, Nawroth P, Ravnskjaer K, Diaz MB, Blagoev B, Herzig S (2021) Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication. Cell Metab. https://doi.org/10.1016/j.cmet.2021.06.005

  51. Schoenfelder S, Fraser P (2019) Long-range enhancer-promoter contacts in gene expression control. Nat Rev Genet 20(8):437–455. https://doi.org/10.1038/s41576-019-0128-0

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank our colleagues from the Functional Genomics and Metabolism Research Unit, University of Southern Denmark for fruitful discussions. The work was supported by grants from the Danish National Research Foundation (DNRF grant No. 141 to the Center for Functional Genomics and Tissue Plasticity (ATLAS) and grants from the Independent Research Fund Denmark. A.L. is supported by a fellowship from the Novo Nordisk Foundation (NNF16OC0020742).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

    Anne Loft, Maja Worm Andersen, Jesper Grud Skat Madsen & Susanne Mandrup

  2. Center for Functional Genomics and Tissue Plasticity (ATLAS), University of Southern Denmark, Odense, Denmark

    Anne Loft, Jesper Grud Skat Madsen & Susanne Mandrup

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  1. Anne Loft
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  2. Maja Worm Andersen
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  3. Jesper Grud Skat Madsen
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  4. Susanne Mandrup
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Correspondence to Anne Loft or Susanne Mandrup .

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  1. Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA

    David A. Guertin

  2. ETH Zürich, Schwerzenbach, Zürich, Switzerland

    Christian Wolfrum

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Loft, A., Andersen, M.W., Madsen, J.G.S., Mandrup, S. (2022). Analysis of Enhancers and Transcriptional Networks in Thermogenic Adipocytes. In: Guertin, D.A., Wolfrum, C. (eds) Brown Adipose Tissue. Methods in Molecular Biology, vol 2448. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2087-8_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2087-8_11

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