Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by chip-seq

Methods in Enzymology

Volumn 537, Issue , 2014, Pages 261-279

  Nielsen, Ronni ^a   Mandrup, Susanne ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Adipocyte; Adipogenesis; ChIP seq; High throughput sequencing; Library preparation; Transcription factors

Indexed keywords

DNA FRAGMENT; TRANSCRIPTION FACTOR;

ADENYLATION; ADIPOCYTE; ARTICLE; BINDING SITE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CROSS LINKING; DNA LIBRARY; DNA REPAIR; DNA SEQUENCE; EPIGENETICS; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; HISTONE MODIFICATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROADIPOCYTE; PROTEIN BINDING; QUALITY CONTROL; QUANTITATIVE ANALYSIS;

ADIPOCYTE; ADIPOGENESIS; CHIP-SEQ; HIGH-THROUGHPUT SEQUENCING; LIBRARY PREPARATION; TRANSCRIPTION FACTORS;

ADIPOCYTES; ADIPOGENESIS; CHROMATIN IMMUNOPRECIPITATION; EPIGENESIS, GENETIC; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; TRANSCRIPTION FACTORS;

EID: 84893191910     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-411619-1.00014-8     Document Type: Chapter

References (34)

1. M. Adli, and B.E. Bernstein Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq Nature Protocols 6 2011 1656 1668
2. A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, and Z. Wang et al. High-resolution profiling of histone methylations in the human genome Cell 129 2007 823 837
3. D.R. Bentley, S. Balasubramanian, H.P. Swerdlow, G.P. Smith, J. Milton, and C.G. Brown et al. Accurate whole human genome sequencing using reversible terminator chemistry Nature 456 2008 53 59
4. A.G. Cristancho, and M.A. Lazar Forming functional fat: A growing understanding of adipocyte differentiation Nature Reviews Molecular Cell Biology 12 2011 722 734
5. S.R. Farmer Transcriptional control of adipocyte formation Cell Metabolism 4 2006 263 273
6. T.S. Furey ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions Nature Reviews Genetics 13 2012 840 852
7. H. Green, and O. Kehinde Sublines of mouse 3T3 cells that accumulate lipid Cell 1 1974 113 116
8. T. Helledie, L. Grontved, S.S. Jensen, P. Kiilerich, L. Rietveld, and T. Albrektsen et al. The gene encoding the acyl-CoA-binding protein is activated by peroxisome proliferator-activated receptor gamma through an intronic response element functionally conserved between humans and rodents Journal of Biological Chemistry 277 2002 26821 26830
9. J.R. Hesselberth, X. Chen, Z. Zhang, P.J. Sabo, R. Sandstrom, and A.P. Reynolds et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting Nature Methods 6 2009 283 289
10. S.G. Landt, G.K. Marinov, A. Kundaje, P. Kheradpour, F. Pauli, and S. Batzoglou et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Genome Research 22 2012 1813 1831
11. M.I. Lefterova, and M.A. Lazar New developments in adipogenesis Trends in Endocrinology & Metabolism 20 2009 107 114
12. M.I. Lefterova, D.J. Steger, D. Zhuo, M. Qatanani, S.E. Mullican, and G. Tuteja et al. Cell-specific determinants of peroxisome proliferator-activated receptor γ function in adipocytes and macrophages Molecular and Cellular Biology 30 2010 2078 2089
13. M.I. Lefterova, Y. Zhang, D.J. Steger, M. Schupp, J. Schug, and A. Cristancho et al. PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale Genes & Development 22 2008 2941 2952
14. G. Li, M. Fullwood, H. Xu, F.H. Mulawadi, S. Velkov, and V. Vega et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Genome Biology 11 2010 R22
15. G. Li, X. Ruan, R.K. Auerbach, K.S. Sandhu, M. Zheng, and P. Wang et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation Cell 148 2012 84 98
16. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, and A. Telling et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
17. T.S. Mikkelsen, Z. Xu, X. Zhang, L. Wang, J.M. Gimble, and E.S. Lander et al. Comparative epigenomic analysis of murine and human adipogenesis Cell 143 2010 156 169
18. R.M. Myers, J. Stamatoyannopoulos, M. Snyder, I. Dunham, R.C. Hardison, and B.E. Bernstein A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biology 9 2011 e1001046
19. R. Nielsen, T.Å. Pedersen, D. Hagenbeek, P. Moulos, R. Siersbæk, and E. Megens et al. Genome-wide profiling of PPARg:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis Genes & Development 22 2008 2953 2967
20. D.E. Nowak, B. Tian, and A.R. Brasier Two-step cross-linking method for identification of NF-kB gene network by chromatin immunoprecipitation Biotechniques 39 2005 715 725
21. B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, and I. Simon et al. Genome-wide location and function of DNA binding proteins Science 290 2000 2306
22. H.S. Rhee, and B.F. Pugh Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Cell 147 2011 1408 1419
23. G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, and T. Zeng et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nature Methods 4 2007 651 657
24. D. Schmidt, M.D. Wilson, C. Spyrou, G.D. Brown, J. Hadfield, and D.T. Odom ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions Methods 48 2009 240 248
25. P.D. Schoppee Bortz, and B.R. Wamhoff Chromatin immunoprecipitation (ChIP): Revisiting the efficacy of sample preparation, sonication, quantification of sheared DNA, and analysis via PCR PLoS ONE 6 2011 e26015
26. P. Shankaranarayanan, M.A. Mendoza-Parra, M. Walia, L. Wang, N. Li, and L.M. Trindade et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq Nature Methods 8 2011 565 567
27. M.S. Siersbæk, A. Loft, M.M. Aagaard, R. Nielsen, S.F. Schmidt, and N. Petrovic et al. Genome-wide profiling of peroxisome proliferator-activated receptor g in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression Molecular and Cellular Biology 32 2012 3452 3463
28. R. Siersbæk, R. Nielsen, S. John, M.H. Sung, S. Baek, and A. Loft et al. Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis EMBO Journal 30 2011 1459 1472
29. R. Siersbæk, R. Nielsen, and S. Mandrup PPARg in adipocyte differentiation and metabolism - Novel insights from genome-wide studies FEBS Letters 584 2010 3242 3249
30. R. Siersbæk, R. Nielsen, and S. Mandrup Transcriptional networks and chromatin remodeling controlling adipogenesis Trends in Endocrinology & Metabolism 23 2012 56 64
31. M.J. Solomon, and A. Varshavsky Formaldehyde-mediated DNA-protein crosslinking: A probe for in vivo chromatin structures Proceedings of the National Academy of Sciences of the United States of America 82 1985 6470
32. D.J. Steger, G.R. Grant, M. Schupp, T. Tomaru, M.I. Lefterova, and J. Schug et al. Propagation of adipogenic signals through an epigenomic transition state Genes & Development 24 2010 1035 1044
33. Z. Zhao, G. Tavoosidana, M. Sjolinder, A. Gondor, P. Mariano, and S. Wang et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions Nature Genetics 38 2006 1341 1347
34. W. Zwart, R. Koornstra, J. Wesseling, E. Rutgers, S. Linn, and J. Carroll A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples BMC Genomics 14 2013 232