Research Publications:
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Weaver, J.R., Good, K., Walters, R.D., Kugel, J.F., and Goodrich, J.A. (2007). Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter. Mol. Immunol. 44: 2813-2819.
Espinoza, C.A., Goodrich, J.A., and Kugel, J.F. (2007). Characterization of the structure, function and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA. 13: 583-596.
Hieb, A.R., Baran, S., Goodrich, J.A., and Kugel, J.F. (2006). An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation. EMBO J. 25: 3100-3109.
Weaver, J.R., Kugel, J.F., and Goodrich, J.A. (2005). The sequence at specific positions in the early transcribed region sets the rate of transcript synthesis by RNA polymerase II in vitro. J. Biol. Chem. 280: 39860-39869.
Espinoza, C.A., Allen, T.A., Hieb, A.R., Kugel, J.F., and Goodrich, J.A. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature Structural and Molecular Biology. 11: 822-829.
Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F. The SINE encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature Structural and Molecular Biology 11: 816-821.
Lively, T.N., Nguyen, T.N., Galasinski, S.K., and Goodrich, J.A. (2004). The basic leucine zipper domain of cJun functions in transcriptional activation through interaction with the N‑terminus of hsTAF1 (human TAF II 250). J. Biol. Chem. 279: 26257-26265.
Kugel, J.F. and Goodrich, J.A. (2003). In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Methods in Enzymology. 370: 687-701.
Kugel, J.F. and Goodrich, J.A. (2002). Translocation after synthesis of a four nucleotide RNA commits RNA polymerase II to promoter escape. Mol. Cell. Biol. 22: 762-773.
Ferguson, H.A., Kugel, J.F., and Goodrich, J.A. (2001). Kinetic and mechanistic analysis of the RNA polymerase II transcription reaction at the human interleukin-2 promoter. J. Mol. Biol. 314: 993-1006.
Ferguson, H.A. and Goodrich, J.A. (2001). Expression and purification of recombinant human c‑Fos/c-Jun that is highly active in DNA binding and transcriptional activation in vitro. Nucleic Acids Res. 29: E98 (6 pages).
Lively, T.N., Ferguson, H.A., Galasinski, S.K., Seto, A.G., and Goodrich, J.A. (2001). c‑Jun binds the N‑terminus of human TAF II 250 to derepress RNA polymerase II transcription in vitro. J. Biol. Chem. 276: 25582-25588.
Kim, L.J., A.G. Seto, T.N. Nguyen, and Goodrich, J.A. (2001). Human TAFII130 is a coactivator for NFATp. Mol. Cell. Biol. 21:3503-3513.-
Kim, L.J., Ferguson, H.A., Seto, A.G., and Goodrich, J.A. (2000). Characterization of DNA binding, transcriptional activation, and regulated nuclear association of recombinant human NFATp. BMC Immunology 1: 1 (10 pages).-
Kugel, J.F. and Goodrich, J.A. (2000). A kinetic model for the early steps of RNA synthesis by human RNA polymerase II. J. Biol. Chem. 275:40483-40491.-
Galasinski, S.K., T.N. Lively, A. Grebe de Barron, and J.A. Goodrich. (2000). Acetyl Coenzyme A stimulates RNA polymerase II transcription and promoter binding by transcription factor IID in the absence of histones. Mol. Cell. Biol. 20: 1923-1930.-
Kugel, J.F. and J.A. Goodrich. (1998). Promoter escape limits the rate of transcription from the adenovirus major late promoter on negatively supercoiled templates. Proc. Natl. Acad. Sci. 95:9232-9237.
Reviews, Methods, Chapters, News and Views:
Kugel, J.F. and Goodrich, J.A. (2007). An RNA transcriptional regulator templates its own regulatory RNA. Nature Chem. Biol. 3: 89-90.
Goodrich, J.A. and Kugel, J.F. (2006). Noncoding RNA regulators of RNA polymerase II transcription. Nature Rev. Mol. Cell Biol. 7: 612-616.
Kugel, J.F. and Goodrich, J.A. (2006). Beating the heat: a translation factor and an RNA mobilize the heat shock transcription factor HSF1. Mol. Cell. 22: 153-154.
Nguyen, T.N. and Goodrich, J.A. (2006). Immobilized protein-protein interaction assays: Eliminating false positive interactions caused by contaminating nucleic acid. Nature Methods. 3: 135-139.
Goodrich, J.A. and Tjian, R. (2006). Transcription: The never ending story. In Gene Expression and Regulation. Ma, J., ed. (Beijing: Higher Education Press and Springer).
Kugel, J.F. and Goodrich, J.A. (2003). In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Methods Enzymol. 370: 687-701
book:
Goodrich, J.A. and Kugel, J.F. (2006). Binding and Kinetics for Molecular Biologists. Cold Spring Harbor Laboratory Press. 182 pages. Computer simulations: http://kinetics.cshl.edu/.