Below are selected papers that have used the ChIP-exo assay (* reported use of Peconic services):
  1. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Rhee HS, Pugh BF. (2012) Nature 483:295-301.
  2. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Rhee HS, Pugh BF. (2012) Curr Protoc Mol Biol Chapter 21:Unit 21 24.
  3. *Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Haimovich G, Medina DA, Causse SZ, Garber M, Millan-Zambrano G, Barkai O, . . . Choder M. (2013) Cell 153:1000-1011.
  4. *A genome-wide map of CTCF multivalency redefines the CTCF code. Nakahashi H, Kwon KR, Resch W, Vian L, Dose M, Stavreva D, . . . Casellas R. (2013) Cell Rep 3:1678-1689.
  5. Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties. Serandour AA, Brown GD, Cohen JD, Carroll JS. (2013) Genome Biol 14:R147.
  6. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Yen K, Vinayachandran V, Pugh BF. (2013) Cell 154:1246-1256.
  7. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination. Carraro N, Matteau D, Luo P, Rodrigue S, Burrus V. (2014) PLoS genetics 10:e1004714.
  8. A comprehensive and high-resolution genome-wide response of p53 to stress. Chang GS, Chen XA, Park B, Rhee HS, Li P, Han KH, . . . Pugh BF. (2014) Cell Rep 8:514-527.
  9. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, . . . Liu Z. (2014) Cell 156:1274-1285.
  10. *​miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression. Escobar TM, Kanellopoulou C, Kugler DG, Kilaru G, Nguyen CK, Nagarajan V, . . . Muljo SA. (2014) Immunity 40:865-879.
  11. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, . . . Tjian R. (2014) eLife 3:e04236.
  12. Subnucleosomal structures and nucleosome asymmetry across a genome. Rhee HS, Bataille AR, Zhang L, Pugh BF. (2014) Cell 159:1377-1388.
  13. *Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling. Wales S, Hashemi S, Blais A, McDermott JC. (2014) Nucleic acids research 42:11349-11362.
  14. Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer. Chen Z, Lan X, Thomas-Ahner JM, Wu D, Liu X, Ye Z, . . . Wang Q. (2015) The EMBO journal 34:502-516.
  15. Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer. Chen Z, Lan X, Wu D, Sunkel B, Ye Z, Huang J, . . . Wang Q. (2015) Nat Commun 6:8323.
  16. The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. Cho S, Cho YB, Kang TJ, Kim SC, Palsson B, Cho BK. (2015) Nucleic acids research 43:3079-3088.
  17. The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway. Fox MJ, Gao H, Smith-Kinnaman WR, Liu Y, Mosley AL. (2015) PLoS genetics 10:e1004999.
  18. CTCF/cohesin-binding sites are frequently mutated in cancer. Katainen R, Dave K, Pitkanen E, Palin K, Kivioja T, Valimaki N, . . . Aaltonen LA. (2015) Nat Genet 47:818-821.
  19. Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo. Lim HW, Uhlenhaut NH, Rauch A, Weiner J, Hubner S, Hubner N, . . . Steger DJ. (2015) Genome Res 25:836-844.
  20. Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo). Matteau D, Rodrigue S. (2015) Methods Mol Biol 1334:173-193.
  21. An ancient protein-DNA interaction underlying metazoan sex determination. Murphy MW, Lee JK, Rojo S, Gearhart MD, Kurahashi K, Banerjee S, . . . Bardwell VJ. (2015) Nat Struct Mol Biol 22:442-451.
  22. Transfer activation of SXT/R391 integrative and conjugative elements: unraveling the SetCD regulon. Poulin-Laprade D, Matteau D, Jacques PE, Rodrigue S, Burrus V. (2015) Nucleic acids research 43:2045-2056.
  23. Molecular mechanisms of ribosomal protein gene coregulation. Reja R, Vinayachandran V, Ghosh S, Pugh BF. (2015) Genes & development 29:1942-1954.
  24. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. (2015) EMBO Rep 16:1673-1687.
  25. *ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, . . . Meijsing SH. (2015) Genome Res 25:825-835.
  26. A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin. Svensson JP, Shukla M, Menendez-Benito V, Norman-Axelsson U, Audergon P, Sinha I, . . . Ekwall K. (2015) Genome research doi:10.1101/gr.188870.114.
  27. ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple-Negative Breast Cancer Cells. Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chan-Salis KY, . . . Wang Y. (2015) Mol Cancer Ther 14:877-888.
  28. *Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis. Wei Y, Mondal SS, Mouawad R, Wilczynski B, Henry RW, Arnosti DN. (2015) G3 (Bethesda) 5:1503-1515.
  29. *Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. Zere TR, Vakulskas CA, Leng Y, Pannuri A, Potts AH, Dias R, . . . Romeo T. (2015) PLoS One 10:e0145035.
  30. Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution. Han GC, Vinayachandran V, Bataille AR, Park B, Chan-Salis KY, Keller CA, . . . Pugh BF. (2016) Mol Cell Biol 36:157-172.
  31. Genomic Organization of Human Transcription Initiation Complexes. Pugh BF, Venters BJ. (2016) PLoS One 11:e0149339.
  32. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Tang X, Liu H, Srivastava A, Pecot T, Chen Z, Wang Q, . . . Leone G. (2016) Sci Data 3:160008.
  33. *Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri. Zhou X, Yan Q, Wang N. (2016) Mol Plant Pathol doi:10.1111/mpp.12397.
  34. Fang, M., and Bauer, C.E. (2017). The Vitamin B12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters. MBio 8,  doi: 10.1128/mBio.00261-17.
  35. *Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease.Gallone, G., Haerty, W., Disanto, G., Ramagopalan, S.V., Ponting, C.P., and Berlanga-Taylor, A.J. (2017).  Hum Mol Genet, 26:2164.
  36. Isakova, A., Groux, R., Imbeault, M., Rainer, P., Alpern, D., Dainese, R., Ambrosini, G., Trono, D., Bucher, P., and Deplancke, B. (2017). SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat Methods 14, 316-322.
  37. Quality of TCR signaling determined by differential affinities of enhancers for the composite BATF-IRF4 transcription factor. Iwata, A., Durai, V., Tussiwand, R., Briseno, C.G., Wu, X., Grajales-Reyes, G.E., Egawa, T., Murphy, T.L., and Murphy, K.M. (2017). Nature Immune 18:563
  38. Simplified ChIP-exo assays. Rossi MJ, Lai WKM, Pugh BF. (2018)  Nat Commun. 9:2842-54.  ​

Below are select papers that have conducted ChIP-exo analysis:
  1. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. Guo Y, Mahony S, Gifford DK. (2012) PLoS computational biology 8:e1002638.
  2. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. (2013) Bioinformatics 29:2705-2713.
  3. A general approach for discriminative de novo motif discovery from high-throughput data. Grau J, Posch S, Grosse I, Keilwagen J. (2013) Nucleic acids research 41:e197.
  4. TherMos: Estimating protein-DNA binding energies from in vivo binding profiles. Sun W, Hu X, Lim MH, Ng CK, Choo SH, Castro DS, . . . Prabhakar S. (2013) Nucleic acids research 41:5555-5568.
  5. Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Carroll TS, Liang Z, Salama R, Stark R, de Santiago I. (2014) Front Genet 5:75.
  6. A new exhaustive method and strategy for finding motifs in ChIP-enriched regions. Jia C, Carson MB, Wang Y, Lin Y, Lu H. (2014) PloS one 9:e86044.
  7. MACE: model based analysis of ChIP-exo. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, . . . Li W. (2014) Nucleic Acids Res 42:e156.
  8. Protein-DNA binding in high-resolution. Mahony S, Pugh BF. (2015) Crit Rev Biochem Mol Biol 50:269-283.
  9. Whole-genome cartography of p53 response elements ranked on transactivation potential. Tebaldi T, Zaccara S, Alessandrini F, Bisio A, Ciribilli Y, Inga A. (2015) BMC Genomics 16:464.
  10. Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Boeva V. (2016) Front Genet 7:24.
  11. Tang, X., Srivastava, A., Liu, H., Huang, K., and Leone, G. (2017). annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq. Bioinformatics. 30:1570
  12. Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony (2019) Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics 35:903
  13. Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ. (2019) In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic Acids Res.46, 8385-8403.