UC San Diego Division of Biological Sciences
Section of Molecular Biology

Kadonaga Lab Publications

Selected Publications

  • Vo ngoc, L., Huang, C. Y., Cassidy, C. J., Medrano, C., and Kadonaga, J. T. (2020). Identification of the human DPR core promoter element using machine learning. Nature 585, 459-363. PMCID: PMC7501168
  • Cruz-Becerra, G., and Kadonaga, J. T. (2020). Enhancement of homology-directed repair with chromatin donor templates in cells. eLife 9, e55780. PMCID: PMC7244325
  • Chavez, C.†, Cruz-Becerra, G. †, Fei, J. †, Kassavetis, G. A. †, and Kadonaga, J. T. (2019). The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. eLife 8, e47682. †Co-first authors. PMCID: PMC6773438
  • Kadonaga, J. T. (2019). The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat. Struct. Mol. Biol. 26, 766-770. PMCID: PMC7025952
  • Vo ngoc, L., Kassavetis, G. A., and Kadonaga, J. T. (2019). The RNA polymerase II core promoter in Drosophila. Genetics 212, 13-24. *Contribution to the Drosophila FlyBook. PMCID: PMC6499525
  • Fei, J., Ishii, H., Hoeksema, M. A., Meitinger, F., Kassavetis, G. A., Glass, C. K., Ren, B., and Kadonaga, J. T. (2018). NDF, a nucleosome destabilizing factor that facilitates transcription through nucleosomes. Genes Dev. 32, 682-694. PMCID: PMC6004073
  • Khuong, M.T., Fei, J., Cruz-Becerra, G., and Kadonaga, J.T. (2017). A simple and versatile system for the ATP-dependent assembly of chromatin. J. Biol. Chem. 292, 19478-19490. PMCID: PMC5702684
  • Vo ngoc, L., Wang, Y.-L., Kassavetis, G.A., and Kadonaga, J.T. (2017). The punctilious RNA polymerase II core promoter. Genes Dev. 31, 1289-1301. PMCID: PMC5580651
  • Vo ngoc, L., Cassidy, C.J., Huang, C.Y., Duttke, S.H.C., and Kadonaga, J.T. (2017). The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. Genes Dev. 31, 6-11. PMCID: PMC5287114
  • Fei, J., Torigoe, S.E., Brown, C.R., Khuong, M.T., Kassavetis, G.A., Boeger, H., and Kadonaga, J.T. (2015). The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev.  29, 2563-2575. PMCID: PMC4699385
  • Khuong, M.T., Fei, J., Ishii, H., and Kadonaga, J.T. (2015). Prenucleosomes and active chromatin. Cold Spring Harbor Symp. Quant. Biol.  80, in press. doi: 10.1101/sqb.2015.80.027300
  • Duttke, S.H.C., Lacadie, S.A., Ibrahim, M.M., Glass, C.K., Corcoran, D.L., Benner, C., Heinz, S., Kadonaga, J.T.‡, and Ohler, U.‡ (2015). Human promoters are intrinsically directional. Mol. Cell  57, 674-684. ‡Co-corresponding authors. PMCID: PMC4336624
  • Ishii, H., Kadonaga, J. T. ‡, and Ren, B. ‡ (2015). MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc. Natl. Acad. Sci. USA   112, E3457-E3465. ‡Co-corresponding authors. PMCID: PMC4500276
  • Duttke, S. H. C., Doolittle, R. F., Wang, Y.-L., and Kadonaga, J. T. (2014). TRF2 and the evolution of the bilateria. Genes Dev.  28, 2071-2076. PMCID: PMC4180970
  • Wang, Y.-L., Duttke, S. H. C., Chen, K., Johnston, J., Kassavetis, G. A., Zeitlinger, J., and Kadonaga, J. T. (2014). TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev.  28, 1550-1555. PMCID: PMC4102762
  • Torigoe, S. E., Patel, A., Khuong, M. T., Bowman, G. D., and Kadonaga, J. T. (2013). ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling. eLife  2, e00863. PMCID: PMC3748710
  • Kadonaga, J. T. (2012). Perspectives on the RNA polymerase II core promoter. WIREs Dev. Biol.  1, 40-51. PMCID: PMC3695423
  • Torigoe, S. E, Urwin, D. L., Ishii, H., Smith, D. E., and Kadonaga, J. T. (2011). Identification of a rapidly formed non-nucleosomal histone-DNA intermediate that is converted into chromatin by ACF. Mol. Cell  43, 638-648. PMCID: PMC3160715
  • Yusufzai, T., and Kadonaga, J. T. (2010). Annealing helicase 2 (AH2), a DNA-rewinding motor with an HNH motif. Proc. Natl. Acad. Sci. USA  107, 20970-20973. PMCID: PMC3000258
  • Parry, T. J., Theisen, J. W. M., Hsu, J.-Y., Wang, Y.-L., Corcoran, D. L., Eustice, M., Ohler, U., and Kadonaga, J. T. (2010). The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes Dev.  24, 2013-2018. PMCID: PMC2939363
  • Juven-Gershon, T., and Kadonaga, J. T. (2010). Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev. Biol. 339, 225-229. PMCID: PMC2830304
  • Yusufzai, T., Kong, X., Yokomori, K., and Kadonaga, J. T. (2009). The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA. Genes Dev.  23, 2400-2404. PMCID: PMC2764493
  • Rattner, B. P., Yusufzai, T., and Kadonaga, J. T. (2009). HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility. Mol. Cell  34, 620-626. PMCID: PMC2709789
  • Yusufzai, T., and Kadonaga, J. T. (2008). HARP is an ATP-driven annealing helicase. Science  322, 748-750. PMCID: PMC2587503
  • Juven-Gershon, T., Hsu, J.-Y., and Kadonaga, J. T. (2008). Caudal, a key developmental regulator, is a DPE-specific transcription factor. Genes Dev.  22, 2823-2830. PMCID: PMC2569877
  • Hsu, J.-Y., Juven-Gershon, T., Marr, M. T., 2nd, Wright, K. J., Tjian, R., and Kadonaga, J. T. (2008). TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes Dev. 22, 2353-2358. PMCID: PMC2532932
  • Santoso, B., and Kadonaga, J. T. (2006). Reconstitution of chromatin transcription with purified components reveals a chromatin-specific repressive activity of p300. Nature Struct. Mol. Biol. 13, 131-139.
  • Lusser, A., Urwin, D. L., and Kadonaga, J. T. (2005). Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nature Struct. Mol. Biol. 12, 160-166.
  • Lim, C. Y., Santoso, B., Boulay, T., Dong, E., Ohler, U., and Kadonaga, J. T. (2004). The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18, 1606-1617.
  • Kadonaga, J. T. (2004). Regulation of RNA polymerase II transcription by sequence-specific DNA-binding factors. Cell 116, 247-257.
  • Fyodorov, D. V., Blower, M. D., Karpen, G. H., and Kadonaga, J. T. (2004). Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 18, 170-183.
  • Alexiadis, V., and Kadonaga, J. T. (2002). Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 16, 2767-2771.
  • Butler, J. E. F., and Kadonaga, J. T. (2002). The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev. 16, 2583-2592.
  • Fyodorov, D. V., and Kadonaga, J. T. (2002). Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418, 897-900.
  • Butler, J. E. F., and Kadonaga, J. T. (2001). Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15, 2515-2519.
  • Willy, P. J., Kobayashi, R., and Kadonaga, J. T. (2000). A basal transcription factor that activates or represses transcription. Science 290, 982-984.
  • Tyler, J. K., Adams, C. R., Chen, S.-R., Kobayashi, R., Kamakaka, R. T., and Kadonaga, J. T. (1999). The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402, 555-560.
  • Ito, T., Levenstein, M. E., Fyodorov, D. V., Kutach, A. K., Kobayashi, R., and Kadonaga, J. T. (1999). ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13, 1529-1539.
  • Blackwood, E. M., and Kadonaga, J. T. (1998). Going the distance: a current view of enhancer action. Science 281, 60-63.
  • Kraus, W. L., and Kadonaga, J. T. (1998). p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 12, 331-342.
  • Burke, T. W., and Kadonaga, J. T. (1997). The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 11, 3020-3031.
  • Ito, T., Bulger, M., Pazin, M. J., Kobayashi, R., and Kadonaga, J. T. (1997). ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145-155.
  • Pazin, M. J., and Kadonaga, J. T. (1997). What’s up and down with histone deacetylation and transcription? Cell 89, 325-328.
  • Pazin, M. J., Bhargava, P., Geiduschek, E. P., and Kadonaga, J. T. (1997). Nucleosome mobility and the maintenance of nucleosome positioning. Science 276, 809-812.
  • Pazin, M. J., and Kadonaga, J. T. (1997). SWI2/SNF2 and related proteins: ATP-driven motors that disrupt protein-DNA interactions? Cell 88, 737-740.
  • Burke, T. W., and Kadonaga, J. T. (1996). Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10, 711-724.
  • Pazin, M. J., Kamakaka, R. T., and Kadonaga, J. T. (1994). ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. Science 266, 2007-2011.
  • Paranjape, S. M., Kamakaka, R. T., and Kadonaga, J. T. (1994). Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu. Rev. Biochem. 63, 265-297.
  • Kamakaka, R. T., Bulger, M., and Kadonaga, J. T. (1993). Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly. Genes Dev. 7, 1779-1795.
  • Tyree, C. M., George, C. P., Lira-DeVito, L. M., Wampler, S. L., Dahmus, M. E., Zawel, L., and Kadonaga, J. T. (1993). Identification of minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 7, 1254-1265.
  • Laybourn, P. J., and Kadonaga, J. T. (1992). Threshold phenomena and long-distance activation of transcription by RNA polymerase II. Science 257, 1682-1685.
  • Laybourn, P. J., and Kadonaga, J. T. (1991). Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science 254, 238-245.
  • Croston, G. E., Kerrigan, L. A., Lira, L., Marshak, D. R., and Kadonaga, J. T. (1991). Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science 251, 643-649.
  • Kamakaka, R. T., Tyree, C. M., and Kadonaga, J. T. (1991). Accurate and efficient RNA polymerase II transcription with a soluble nuclear fraction derived from Drosophila embryos. Proc. Natl. Acad. Sci. USA 88, 1024-1028.
  • Kadonaga, J. T., Courey, A. J., Ladika, J., and Tjian, R. (1988). Distinct regions of Sp1 modulate DNA binding and transcriptional activation. Science 242, 1566-1570.
  • Kadonaga, J. T., Carner, K. R., Masiarz, F. R., and Tjian, R. (1987). Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell 51, 1079-1090.
  • Kadonaga, J. T., and Tjian, R. (1986). Affinity purification of sequence-specific DNA binding proteins. Proc. Natl. Acad. Sci. USA 83, 5889-5893.