ChIP on Chip

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Contact:
Lee Edsall
ledsall@ucsd.edu

Publications on in ChIP-on-chip experiments

Listed here are a few review and research articles published on ChIP-chip experiments:

Reviews (ordered by date of publication)

  1. Horak, C.E. and M. Snyder, ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol, 2002. 350: p. 469-83. [PMID:12073330]
  2. Wyrick, J.J. and R.A. Young, Deciphering gene expression regulatory networks. Curr Opin Genet Dev, 2002. 12(2): p. 130-6. [PMID:1189348 4]
  3. Weinmann, A.S. and P.J. Farnham, Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods, 2002. 26(1): p. 37-47. [PMID:12054903]
  4. Lieb, J.D., Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization. Methods Mol Biol, 2003. 224: p. 99-109. [PMID:12710669]
  5. Oberley, M.J. and P.J. Farnham, Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol, 2003. 371: p. 577-96. [PMID:14712730]
  6. Kurdistani, S.K. and M. Grunstein, In vivo protein-protein and protein-DNA crosslinking for genomewide binding microarray. Methods, 2003. 31(1): p. 90-5. [PMID:12893178]
  7. Ren, B. and B.D. Dynlacht, Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Methods Enzymol, 2004. 376: p. 304-15. [PMID:14975314]
  8. Robyr, D., S.K. Kurdistani, and M. Grunstein, Analysis of genome-wide histone acetylation state and enzyme binding using DNA microarrays. Methods Enzymol, 2004. 376: p. 289-304. [PMID:14975313]
  9. Hanlon, S.E. and J.D. Lieb, Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev, 2004. 14(6): p. 697-705. [PMID:15531167]
  10. Boguski, M.S., ENCODE and ChIP-chip in the genome era. Genomics, 2004. 83(3): p. 347-8. [PMID:14962661]
  11. Buck, M.J. and J.D. Lieb, ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 2004. 83(3): p. 349-60. [PMID:14986705]
  12. Weinmann, A.S., Novel ChIP-based strategies to uncover transcription factor target genes in the immune system. Nat Rev Immunol, 2004. 4(5): p. 381-6. [PMID:15122203]

Research articles (ordered by date of publication):

  1. Blat, Y. and N. Kleckner, Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell, 1999. 98(2): p. 249-59. [PMID:10428036]
  2. Ren, B., F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T.L. Volkert, C.J. Wilson, S.P. Bell, and R.A. Young, Genome-wide location and function of DNA binding proteins. Science, 2000. 2 90(5500): p. 2306-9. [PMID:11125145]
  3. Lieb, J.D., X. Liu, D. Botstein, and P.O. Brown, Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet, 2001. 28(4): p. 327-34. [PMID:11455386]
  4. Wyrick, J.J., J.G. Aparicio, T. Chen, J.D. Barnett, E.G. Jennings, R.A. Young, S.P. Bell, and O.M. Aparicio, Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science, 2001. 294(5550): p . 2357-60. [PMID:11743203]
  5. Iyer, V.R., C.E. Horak, C.S. Scafe, D. Botstein, M. Snyder, and P.O. Brown, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 2001. 409(6819): p. 533-8. [PMID:11206552]
  6. Simon, I., J. Barnett, N. Hannett, C.T. Harbison, N.J. Rinaldi, T.L. Volkert, J.J. Wyrick, J. Zeitlinger, D.K. Gifford, T.S. Jaakkola, and R.A. Young, Serial regulation of transcriptional regulators in the yeast cell cycle. Cell, 2001. 106(6): p. 697- 708. [PMID:11572776]
  7. Ng, H.H., F. Robert, R.A. Young, and K. Struhl, Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev, 2002. 16(7): p. 806-19. [PMID:11937489]
  8. Liu, X.S., D.L. Brutlag, and J.S. Liu, An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol, 2002. 20(8): p. 835-9. Epub 2002 Jul 08. [PMID:12101404]
  9. Ren, B., H. Cam, Y. Takahashi, T. Volkert, J. Terragni, R.A. Young, and B.D. Dynlacht, E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev, 2002. 16(2): p. 245-56. [PMID:11799067]
  10. Weinmann, A.S., P.S. Yan, M.J. Oberley, T.H. Huang, and P.J. Farnham, Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev, 2002. 16(2): p. 235-44. [PMID:11799066]
  11. Kurdistani, S.K., D. Robyr, S. Tavazoie, and M. Grunstein, Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet, 2002. 31(3): p. 248-54. Epub 2002 Jun 24. [PMID:12089521]
  12. Bernstein, B.E., E.L. Humphrey, R.L. Erlich, R. Schneider, P. Bouman, J.S. Liu, T. Kouzarides, and S.L. Schreiber, Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A, 2002. 99(13): p. 8695-700. Epub 2002 Jun 11 . [PMID:12060701]
  13. Robyr, D., Y. Suka, I. Xenarios, S.K. Kurdistani, A. Wang, N. Suka, and M. Grunstein, Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell, 2002. 109(4): p. 437-46. [PMID:12086601]
  14. Lee, T.I., N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel, D.K. G ifford, and R.A. Young, Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 2002. 298(5594): p. 799-804. [PMID:123995 84]
  15. Sun, L.V., L. Chen, F. Greil, N. Negre, T.R. Li, G. Cavalli, H. Zhao, B. Van Steensel, and K.P. White, Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci U S A, 2003. 100(16): p. 9428-33. Epub 2003 Jul 22. [PMID:12876199]
  16. Li, Z., S. Van Calcar, C. Qu, W.K. Cavenee, M.Q. Zhang, and B. Ren, A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc Natl Acad Sci U S A, 2003. 100(14): p. 8164-9. Epub 2003 Jun 13. [PMID:12808131]
  17. Ng, H.H., F. Robert, R.A. Young, and K. Struhl, Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell, 2003. 11(3): p. 709-19. [PMID:12667453]
  18. Wells, J., P.S. Yan, M. Cechvala, T. Huang, and P.J. Farnham, Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene, 2003. 22(10): p. 1445-60. [PMID:12629508]
  19. Zeitlinger, J., I. Simon, C.T. Harbison, N.M. Hannett, T.L. Volkert, G.R. Fink, and R.A. Young, Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell, 2003. 113(3): p. 395-404. [PMI D:12732146]
  20. Mao, D.Y., J.D. Watson, P.S. Yan, D. Barsyte-Lovejoy, F. Khosravi, W.W. Wong, P.J. Farnham, T.H. Huang, and L.Z. Penn, Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression. Curr Biol, 2003 . 13(10): p. 882-6. [PMID:12747840]
  21. Martone, R., G. Euskirchen, P. Bertone, S. Hartman, T.E. Royce, N.M. Luscombe, J.L. Rinn, F.K. Nelson, P. Miller, M. Gerstein, S. Weissman, and M. Snyder, Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A, 20 03. 100(21): p. 12247-52. Epub 2003 Oct 03. [PMID:14527995]
  22. Bernstein, B.E., E.L. Humphrey, C.L. Liu, and S.L. Schreiber, The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol, 2004. 376: p. 349-60. [PMID:14975317]
  23. Bernstein, B.E., C.L. Liu, E.L. Humphrey, E.O. Perlstein, and S.L. Schreiber, Global nucleosome occupancy in yeast. Genome Biol, 2004. 5(9): p. R62. Epub 2004 Aug 20. [PMID:15345046]
  24. Oberley, M.J., J. Tsao, P. Yau, and P.J. Farnham, High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Methods Enzymol, 2004. 376: p. 315-34. [PMID:14975315]
  25. Lee, C.K., Y. Shibata, B. Rao, B.D. Strahl, and J.D. Lieb, Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet, 2004. 36(8): p. 900-5. Epub 2004 Jul 11. [PMID:15247917]
  26. White, E.J., O. Emanuelsson, D. Scalzo, T. Royce, S. Kosak, E.J. Oakeley, S. Weissman, M. Gerstein, M. Groudine, M. Snyder, and D. Schubeler, DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A, 2004. [PMID:15591350]
  27. Cawley, S., S. Bekiranov, H.H. Ng, P. Kapranov, E.A. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, J. Cheng, A.J. Williams, R. Wheeler, B. Wong, J. Drenkow, M. Yamanaka, S. Patel, S. Brubaker, H. Tammana, G. Helt, K. Struhl, and T.R. Gingeras, U nbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 2004. 116(4): p. 499-509. [PMID:14980218]
  28. Odom, D.T., N. Zizlsperger, D.B. Gordon, G.W. Bell, N.J. Rinaldi, H.L. Murray, T.L. Volkert, J. Schreiber, P.A. Rolfe, D.K. Gifford, E. Fraenkel, G.I. Bell, and R.A. Young, Control of pancreas and liver gene expression by HNF transcription factors. Sc ience, 2004. 303(5662): p. 1378-81. [PMID:14988562]
  29. Kirmizis, A., S.M. Bartley, A. Kuzmichev, R. Margueron, D. Reinberg, R. Green, and P.J. Farnham, Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev, 2004. 18(13): p. 1592-605. [PMID:15231737]
  30. Hahn, J.S., Z. Hu, D.J. Thiele, and V.R. Iyer, Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol, 2004. 24(12): p. 5249-56. [PMID:15169889]
  31. Schubeler, D., D.M. MacAlpine, D. Scalzo, C. Wirbelauer, C. Kooperberg, F. van Leeuwen, D.E. Gottschling, L.P. O'Neill, B.M. Turner, J. Delrow, S.P. Bell, and M. Groudine, The histone modification pattern of active genes revealed through genome-wide c hromatin analysis of a higher eukaryote. Genes Dev, 2004. 18(11): p. 1263-71. [PMID:15175259]
  32. Kurdistani, S.K., S. Tavazoie, and M. Grunstein, Mapping global histone acetylation patterns to gene expression. Cell, 2004. 117(6): p. 721-33. [PMID:15186774]
  33. Euskirchen, G., T.E. Royce, P. Bertone, R. Martone, J.L. Rinn, F.K. Nelson, F. Sayward, N.M. Luscombe, P. Miller, M. Gerstein, S. Weissman, and M. Snyder, CREB binds to multiple loci on human chromosome 22. Mol Cell Biol, 2004. 24(9): p. 3804-14. [PM ID:15082775]
  34. Moqtaderi, Z. and K. Struhl, Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol, 2004. 24(10): p. 4118-27. [PMID:15121834]
  35. Hall, D.A., H. Zhu, X. Zhu, T. Royce, M. Gerstein, and M. Snyder, Regulation of gene expression by a metabolic enzyme. Science, 2004. 306(5695): p. 482-4. [PMID:15486299]
  36. Robert, F., D.K. Pokholok, N.M. Hannett, N.J. Rinaldi, M. Chandy, A. Rolfe, J.L. Workman, D.K. Gifford, and R.A. Young, Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell, 2004. 16(2): p. 199-209. [PMID:15494307]
  37. Kim, J. and V.R. Iyer, Global role of TATA box-binding protein recruitment to promoters in mediating gene expression profiles. Mol Cell Biol, 2004. 24(18): p. 8104-12. [PMID:15340072]
  38. Harbison, C.T., D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraen kel, and R.A. Young, Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104. [PMID:15343339]