View our lablog for major events, milestones and achievements. You can also view our publications and their citations on Google Scholar or PubMed and view/download our genomic data at ArrayExpress. We have a broad interest in genome function and control. Transcription insulation and elongation mechanisms in the human genome are the current focus of our research.


Publications

  1. Tae Hoon Kim. Expression of Salt Tolerance Genes in Vibrio costicola. BASE: A Journal of Science and Technology 8:6-10 (1990). 

  2. Tae Hoon Kim. Programmed Cell Death in Arabidopsis thaliana. Reed College. Portland (1994).

  3. Tae Kook Kim, Tae Hoon Kim, and Tom Maniatis. Efficient recruitment of TFIIB and CBP-RNA polymerase II holoenzyme by an Interferon-β enhanceosome in vitro. Proceedings of National Academy of Sciences, USA 95:12191-96 (1998). 

  4. Tom Maniatis, James Falvo, Tae Hoon Kim, Tae Kook Kim, Charles H. Lin, Bhavin S. Parekh, and Marc G. Wathelet. Structure and function of the interferon-β enhanceosome. Cold Spring Harbor Symposium on Quantitative Biology 63:609-620 (1998).

  5. Bing Ren, Kerlen J. Chee, Tae Hoon Kim, and Tom Maniatis. PRDI-BF1/Blimp-1 repression is mediated by corepressors of the groucho family of proteins. Genes and Development 13:125-137 (1999).

  6. Tae Hoon Kim. Structure and Function of Enhanceosome. Harvard University. Cambridge (2002).

  7. The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306:636-640 (2004).

  8. Tae Hoon Kim, Hui Xong, Zhuohua Zhang, and Bing Ren. β-catenin activates the growth factor endothelin-1 in colon cancer cells. Oncogene 24:597-604 (2005).

  9. Tae Hoon Kim, Leah O. Barrera, Chunxu Qu, Sara Van Calcar, Nathan Trinklein, Sarah Hartman, Rosa Luna, Christopher K. Glass, Michael G. Rosenfeld, Richard Myers, and Bing Ren. Direct isolation and identification of promoters in the human genome. Genome Research 15:830-839 (2005).

  10. Tae Hoon Kim, Leah O. Barrera, Ming Zheng, Chunxu Qu, Michael A. Singer, Todd A. Richmond, Yingnian Wu, Roland Green, and Bing Ren. A high-resolution map of active promoters in the human genome. Nature 436:876-880 (2005).

  11. Ping Sun, Hui Xiong, Tae Hoon Kim, Bing Ren, and Zhuohua Zhang. Positive Inter-Regulation between Beta-Catenin/T Cell Factor-4 Signaling and Endothelin-1 Signaling Potentiates Proliferation and Survival of Prostate Cancer Cells. Molecular Pharmacology 69:520-31 (2006).

  12. Tae Hoon Kim and Bing Ren. All-around view of eukaryotic transcription. Genome Biology 7:323 (2006).

  13. Tae Hoon Kim* and Bing Ren*. Genome-wide Analysis of Protein-DNA Interactions. Annual Review of Genomics and Human Genetics 7:81-102 (2006). *corresponding authors

  14. Tae Hoon Kim*, Ziedulla Abdullayev, Keith A. Ching, Andrew Smith, Dmitri Loukinov, Roland D. Green, Michael Q. Zhang, Victor Lobanenkov and Bing Ren*. Analysis of the vertebrate insulator protein CTCF binding sites in the human genome. Cell 128:1231-1245 (2007). *corresponding authors

  15. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816 (2007).

  16. Tae Hoon Kim*, Leah O. Barrera and Bing Ren*. ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Current Protocols in Molecular Biology 79 Unit 21.13 (2007). *corresponding authors

  17. Tae Hoon Kim: knows his boundaries. Interview by Ruth Williams. Journal of Cell Biology 183:4-5 (2008).

  18. Kerrigan B. Gilbert, Tae Hoon Kim, Rashmi Gupta, E. P. Greenberg, and Martin Schuster. Global position analysis of the Pseudomonas aeruginosa quorum-sensing transcription factor LasR. Molecular Microbiology 73:1072-1085 (2009).

  19. David A. Wacker and Tae Hoon Kim. From Sextant to GPS: Twenty-five Years of Mapping the Genome with ChIP. Journal of Cellular Biochemistry 107:6-10 (2009).

  20. Katharine R. Cecchini, A. Raja Banerjee and Tae Hoon Kim. Toward a genome-wide reconstruction of cis-regulatory networks in the human genome. Seminars in Cell and Developmental Biology 20:842-848 (2009).

  21. David A. Wacker, Yoon Jung Kim and Tae Hoon Kim. Chromatin modifications distinguish genomic features and physical organization of the nucleus. in Handbook of Epigenetics: The New Molecular and Medical Genetics (ed. T. Tollefsbol). Elsevier Academic Press (2010).

  22. Yoon Jung Kim, Katharine R. Cecchini and Tae Hoon Kim. Conserved, developmentally regulated mechanism couples chromosomal looping and heterochromatin barrier activity at the homeobox gene A locus. Proceedings of National Academy of Sciences, USA 108:7391-7396 (2011).

  23. Bora E. Baysal, Sharen E. McKay, Yoon Jung Kim, Zimei Zhang, Linda Alila, Joan E. Willett-Brozick, Karel Pacak, Tae Hoon Kim and Gerald S. Shadel. Genomic imprinting at a boundary element flanking the SDHD locus. Human Molecular Genetics 20:4452-4461 (2011).

  24. Tae Hoon Kim* and Job Dekker*. Crosslinking Technologies for Analysis of Chromatin Structure and Function. in Molecular Cloning: A Laboratory Manual (ed. M. R. Green  and J. Sambrook). Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2012). *corresponding authors

  25. Yoon Jung Kim*, Celeste Greer*, Katharine Cecchini, Lyndsay N. Harris, David P. Tuck and Tae Hoon Kim. HDAC inhibitors induce transcriptional repression of high copy number genes in breast cancer through elongation blockade. Oncogene 32: 2828-2835 (2013). *equal contribution

  26. Lark Kyun Kim, Enric Esplugues, Cornelia E. Zorca, Fabio Parisi, Yuval Kluger, Tae Hoon Kim, Niels J. Galjart, and Richard A. Flavell. Oct-1 regulates IL-17 expression by directing interchromosomal associations in conjunction with CTCF in T cells. Molecular Cell 54:56-66 (2014).

  27. Tae Hoon Kim* and Job Dekker*. Protein-DNA Interactions. in Molecular Neuroscience (ed. Rusty Lansford). Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2014). *corresponding authors

  28. A. Raja Banerjee*, Yoon Jung Kim* and Tae Hoon Kim. A novel virus-inducible enhancer of the interferon gene with tightly linked promoter and enhancer activities. Nucleic Acids Research 42:12537-54 (2014).*equal contribution
  29. Ifeoma Jane Nwigwe, Yoon Jung Kim, David A. Wacker and Tae Hoon Kim. Boundary associated long noncoding RNA mediates long-range chromosomal interactions. PLoS ONE 10(8):e0136104 (2015).

  30. Celeste B. Greer, Yoshiaki Tanaka, Yoon Jung Kim, Peng Xie, Michael Q. Zhang, In-Hyun Park and Tae Hoon Kim. Histone deacetylases positively regulate transcription through the elongation machinery. Cell Reports 13:1444-1455 (2015).

    • GRO-seq and ChIP-seq data are available at ArrayExpress repository
  31. Qianqian Ye, Yoon Jung Kim, Hongyu Zhao and Tae Hoon Kim. Three distinct velocities of elongating RNA polymerase define exons and introns. bioRxiv doi: http://dx.doi.org/10.1101/044123 (2016).
    • GRO-seq, mRNA-seq and ChIP-seq data are available at ArrayExpress repository
  32. Justin L. Tan, Rachel D. Fogley, Ryan A. Flynn, Julien Ablain, Song Yang, Violaine Saint-André, Zi Peng Fan, Brian T. Do, Alvaro C. Laga, Koh Fujinaga, Cristina Santoriello, Celeste B. Greer, Yoon Jung Kim, John G. Clohessy, Anne Bothmer, Nicole Pandell, Serine Avagyan, John E. Brogie, Ellen van Rooijen, Elliot J. Hagedorn, Ng Shyh-Chang, Richard M. White, David H. Price, Pier Paolo Pandolfi, B. Matija Peterlin, Yi Zhou, Tae Hoon Kim, John M. Asara, Howard Y. Chang, Richard A. Young and Leonard I. Zon. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Molecular Cell 62:34-46 (2016).

  33. Boksik Cha, Xin Geng, Md. Riaj Mahamud, Jianxin Fu, Anish Mukherjee, Yeunhee Kim, Eek-hoon Jho, Tae Hoon Kim, Mark L. Kahn, Lijun Xia, J. Brandon Dixon, Hong Chen, and R. Sathish Srinivasan. Mechanotransduction activates canonical Wnt/β-catenin signaling to promote lymphatic vascular patterning and the development of lymphatic and lymphovenous valves. Genes & Development 30:1454-1469 (2016).

  34. Yoon Jung Kim and Tae Hoon Kim. Chromosome Conformation Capture for Research on Innate Antiviral Immunity. in Innate Antiviral Immunity: Methods and Protocols, Methods in Molecular Biology, vol. 1656 (ed. Karen Mossman). Springer (2017).