Publications
Archuleta, S.R., Goodrich, J.A., and Kugel, J.F. (2024) Mechanisms and functions of the RNA polymerase II general transcription machinery during the transcription cycle. Biomolecules. 14:176.
Miller, G.M., Brant, T.S., Goodrich, J.A., and Kugel, J.F. (2023) Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. FEBS Open Bio. 13:1941-1952.
Suwita, J.P., Voong, C.K., Ly, E., Goodrich, J.A., and Kugel, J.F. (2023) Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements. PLoS One. 18:e0286193.
Scott, A.K., Casas, E., Schneider, S.E., Swearingen, A.R., Van Den Elzen, C.L., Seelbinder, B., Barthold, J.E., Kugel, J.F., Stern, J.L., Foster, K.J., Emery, N.C., Brumbaugh, J., Neu, C.P. (2023) Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophys. J. 122:1428-1444.
Singh, A., Miller, R.C., Archuleta, S.R., and Kugel, J.F. (2023) Evaluating two steps in transcription using a fluorescence-based electrophoretic mobility shift assay. Biochem. Mol. Biol. Educ. 51:230-235.
Hemphill, W.O., Voong, C.K., Fenske, R., Goodrich, J.A., Cech, T.R. (2023) Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search. Proc Natl Acad Sci USA. 120:e2220537120.
Bosire, R., Fadel, L., Mocsár, G., Nánási, P., Sen, P., Sharma, A.K., Naseem, M.U., Kovács, A., Kugel, J., Kroemer, G., Vámosi, G., and Szabó, G. (2022) Doxorubicin impacts the chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Sci Rep.
Voong C.K., Goodrich, J.A., and Kugel, J.F. (2021) Interactions of HMGB proteins with the genome and the impact on disease. Biomolecules. 11:1451.
Rivas, T., Goodrich, J.A., and Kugel, J.F. (2021) The herpes simplex virus 1 protein ICP4 acts as both an activator and repressor of host genome transcription during infection. Mol. Cell. Biol. 24:e0017121.
Salant, G.M., Tat, K.L., Goodrich, J.A., and Kugel, J.F. (2020) miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs. RNA Biol.7: 956-965.
Ly, E., Kugel, J.F., and Goodrich, J.A. (2020) Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Sci. Rep. 10:16176.
Ly, E., Powell, A.E., Goodrich, J.A., and Kugel, J.F. (2020) Release of human TFIIB from actively transcribing complexes is triggered upon synthesis of 7 nt and 9 nt RNAs. J. Mol. Biol. 432: 4049-4060.
Greene, E., Flees, J., Dhamad, A., Alrubaye, A., Hennigan, S., Pleimann, J., Smeltzer, M., Murray, S., Kugel, J.F., Goodrich, J., Robertson, A., Wideman, R., Rhoads, D., and Dridi, S. (2019) Double-stranded RNA is a novel molecular target in osteomyelitis pathogenesis. Am. J. Pathol. 189:2077-2089. .
Ly, E., Goodrich, J.A., and Kugel, J.F. (2019) Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization. Methods. S1046-2023(18):30302-5.
Cardiello, J.F., Goodrich, J.A., and Kugel, J.F. (2018) Heat shock causes a reversible increase in RNA polymerase II occupancy downstream of mRNA genes, consistent with a global loss in transcriptional termination. Mol. Cell. Biol. 38:e00181-18.
Goodrich J.A. and Taatjes, D. (2018) Transcription regulation enters a new phase. Nature. 558:197-198.
Kugel, J.F. and Goodrich, J.A. (2017) Finding the start site: redefining the human initiator element. Genes Dev. 31:1-2.
Blair, R.H., Horn, A.E., Pazhani, Y., Grado, L., Goodrich, J.A., and Kugel, J.F. (2016) The HMGB1 C-Terminal Tail Regulates DNA Bending. J. Mol. Biol. 428:4060-4072.
Horn, A.E., Kugel, J.F., Goodrich, J.A. (2016) Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity. Nucl. Acids Res. 44:7132-43.
Eidem, T.M., Kugel, J.F., and Goodrich, J.A. (2016) Noncoding RNAs: Regulators of the mammalian transcription machinery. J. Mol. Biol. 428:2652-2659.
Abrisch, R.G., Eidem, T.M., Yakovchuk, P., Kugel, J.F., and Goodrich, J.A. (2016) Infection by Herpes Simplex Virus Type-I causes near-complete loss of RNA polymerase II occupancy on the host cell genome. J. Virol. 90:2503-2513.
Pazhani, Y., Horn, A.E., Grado, L., and Kugel, J.F. (2016) Evaluating the relationship between FRET changes and distance changes using DNA length and restriction enzyme specificity. J. Chem. Edu. 93:383-386.
Ponicsan, S.L., Kugel, J.F., and Goodrich, J.A. (2015) Repression of RNA Polymerase II Transcription by B2 RNA Depends on a Specific Pattern of Structural Regions in the RNA. Non-coding RNA. 1:4-16.
Goodrich, J.A., and Kugel, J.F. (2015) Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINEncRNA/Pol II complexes as a model system. Meth. Mol. Biol. 1206:165-178.
Cardiello, J.F., Kugel, J.F., and Goodrich, J.A. (2014) A new twist on cell growth control. Cell Cycle. 13:3474-3475.
Walters, R.D., McSwiggen, D.T, Goodrich, J.A., and Kugel, J.F. (2014) Selection and characterization of a DNA aptamer that can discriminate between cJun/cJun and cJun/cFos. PLOS ONE. 9:e101015.
Horn, A.E., Goodrich, J.A., and Kugel, J.F. (2014) Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 5:e27608.
Walters, R.D., Drullinger, L.F., Kugel, J.F., and Goodrich J.A. (2013) NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription. Mol. Immunol. 46:48-56.
Ponicsan, S.L., Houel, S., Old, W.M., Ahn, N.G., Goodrich, J.A., Kugel, J.F. (2013) The non-coding B2 RNA binds to the DNA cleft and active site region of RNA polymerase II. J.Mol. Biol. 425:3625-3638.
Thrall, J.M.H. and Goodrich, J.A. (2013) Promoters. In Brenner's Encyclopedia of Genetics, 2nd Edition. Maloy, S. and Hughes, K., eds. (Elsevier Press)
Wagner, S.D., Yakovchuk, P., Gilman, B., Poniscan, S.L., Drullinger, L.F., Kugel, J.F., and Goodrich, J.A. (2013) Mammalian RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J. 32:781-90.
Blair, R.H., Goodrich, J.A., and Kugel, J.F. (2013) Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system. Meth. Mol. Biol. 977:203-215.
Kugel, J.F. and Goodrich J.A. (2013). The regulation of mammalian mRNA transcription by long non-coding RNAs: Recent discoveries and current concepts. Epigenomics. 5:95-102.
Kassube, S.A., Fang, J., Grob, P., Yakovchuk, P., Goodrich, J.A., and Nogales, E. (2013) Structural insights into transcriptional repression by ncRNAs that bind to human Pol II. J. Mol. Biol. 425:3639-3648.
Heffler M.A., Walters, R.D., and Kugel, J.F. (2012) Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4-p53 binding DNA as a model system. Biochem. Mol. Biol. Educ. 40:383-387.
Blair, R.H., Goodrich, J.A., and Kugel, J.F. (2012) Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics. Biochemistry 51:7444-7455.
Dridi, S., Hirano, Y., Tarallo, V., Kim, Y., Fowler, B.J., Ambati, B.K., Bogdanovich, S., Chiodo, V.A., Hauswirth, W.W., Kugel, J.F., Goodrich, J.A., Ponicsan, S.L., Hinton, D.R., Kleinman, M.E., Baffi, J., Gelfand, B.D., and Ambati, J. (2012) ERK1/2 activation is a therapeutic target in age-related macular degeneration. Proc. Natl. Acad. Sci. USA. 109:13781-13786.
Tarallo, V., Hirano, Y., Gelfand, B.D., Dridi, S., Kerur, N., Kim, Y., Cho, W.G., Kaneko, H., Fowler, B.J., Bogdanovich, S., Albuquerque, R.J.C., Hauswirth, W.W., Chiodo, V.A., Kugel, J.F., Goodrich, J.A., Ponicsan, S.L., Chaudhuri, G., Murphy, M.P., Dunaief, J., Ambati, B.K., Ogura, Y., Yoo, J.W., Lee, D.K., Provost, P., Hinton, D.R., Núñez, G., Baffi, J., Kleinman, M.E., and Ambati, J. (2012) DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell 149:847-859.
Kugel, J.F. and Goodrich, J.A. (2012) Non-coding RNAs: key regulators of mammalian transcription. Trends in Biochem. Sci. 37:144-151.
Kaneko, H., Dridi, S., Tarallo, V., Fowler, B.J., Gelfand, B.D., Cho, W.G., Kleinman, M.E., Ponicsan, S.L., Hauswirth, W.H., Chiodo, V.A., Karikó, K., Yoo, J.W., Lee, D.-K., Hadziahmetovic, M., Song, Y., Chaudhuri, G., Buaas, F.W., Braun, R.E., Hinton, D.R., Zhang, Q., Grossniklaus, H.E., Provis, J.M., Madigan, M.C., Milam, A.H., Justice, N.L., Albuquerque, R.J.C., Blandford, A.D., Bogdanovich, S., Hirano, Y., Witta, J., Fuchs, E., Littman, D.R., Ambati, B.K., Rudin, C.M., Chong, M.M.W., Provost, P., Kugel, J.F., Goodrich, J.A., Dunaief, J.L., Baffi, J.Z., Ambati, J. (2011). DICER1 dysregulation induces cytotoxic AluRNA accumulation in age-related macular degeneration. Nature. 471:325-330.
Titov, D.V., Gilman, B., He, Q.-L., Bhat, S., Low, W.-K., Dang, Y., Smeaton, M., Demain, A.J., Miller, P.S., Kugel, J.F., Goodrich, J.A., Liu, J.O. (2011). XPB, a subunit of TFIIH, is a target of the natural product triptolide. Nat. Chem. Biol. 7:182-188.
Yakovchuk, P., Goodrich J.A., and Kugel, J.F. (2011) B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription. 2:45-49.
Nguyen, T.N., Kim, L.J., Walters, R.D., Drullinger, L.F., Lively, T.N., Kugel, J.F., and Goodrich, J.A. (2010) The C-terminal region of human NFATc2 binds cJun to synergistically activate interleukin-2 transcription. Mol Immunol. 47: 2314-2322.
Goodrich, J.A. and Kugel, J.F. (2010) Genome-wide insights into eukaryotic transcriptional control. Genome Biol. 11:305.
Goodrich, J.A. and Tjian, R. (2010) Unexpected roles for core promoter recognition factors in cell-type specific transcription and gene regulation. Nature Reviews Genetics. 11: 549-558.
Goodrich, J.A. and Kugel, J.F. (2010) Dampening DNA binding: A common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biol. 7:305-309.
Ponicsan, S.L., Kugel, J.F., and Goodrich, J.A. (2010) Genomic gems: SINE RNAs regulate mRNA production. Curr. Opin. Gen. Dev. 20: 149-155.
Yakovchuk, P., Gilman, B., Goodrich, J.A., and Kugel, J.F. (2010) RNA polymerase II and TAFs undergo a slow isomerization after the polymerase is recruited to promoter-bound TFIID. J. Mol. Biol. 397: 57-68.
Wagner, S.D., Kugel, J.F., and Goodrich, J.A. (2010) TFIIF facilitates dissociation of RNA polymerase II from non-coding RNAs that lack a repression domain. Mol. Cell. Biol. 30: 91-97.
Walters, R.D., Kugel, J.F., and Goodrich, J.A. (2009) InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life. 61: 831-837.
Kugel, J.F. and Goodrich, J.A. (2009) In new company: U1 snRNA associates with TAF15. EMBO rep. 10: 454-456.
Yakovchuk, P, Goodrich, J.A., and Kugel, J.F. (2009) B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc. Natl. Acad. Sci. USA. 106: 5569-5574.
Gilman, B, Drullinger, L.F., Kugel, J.F., and Goodrich, J.A. (2009) TATA-binding protein and transcription factor IIB induce transcript slipping during early transcription by RNA polymerase II. J. Biol. Chem. 284: 9093-9098.
Goodrich, J.A. and Kugel, J.F. (2009) From bacteria to humans, chromatin to elongation, and activation to repression: the expanding roles of noncoding RNAs in regulating transcription. Crit. Rev. Biochem. Mol. Biol. 44: 3-15.
Kugel, J.F. (2008) Using FRET to measure the angle at which a protein bends DNA. Biochem. Mol. Biol. Educ. 36: 341-346.
Mariner, P.D., Walters, R.D., Espinoza, C.A., Drullinger, L.F., Wagner, S.D., Kugel, J.F., and Goodrich, J.A. (2008) Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol. Cell 29: 499-509.
Wager, S.D., Kugel, J.F., and Goodrich, J.A. (2008) The role of non-coding RNAs in controlling mammalian RNA polymerase II transcription. Chapter 9 in RNA and the Regulation of Gene Expression, Editor K. Morris, Horizon Scientific Press, Norwich, UK.
Hieb, A.R., Halsey, W.A., Betterton, M., Perkins, T., Kugel, J.F., and Goodrich, J.A. (2007) TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J. Mol. Biol. 372: 619-632.
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: 783-596.
Kugel, J.F. and Goodrich, J.A. (2007) An RNA transcriptional regulator templates its own regulatory RNA. Nat. Chem. Biol. 3: 89-90.
Goodrich, J.A. and Kugel, J.F. (2007) Binding and Kinetics for Molecular Biologists. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY. 182 pages.
Hofmann, W.A., Vargas, G.M., Ramchandran, R., Ljuba, S., Goodrich, J.A., and de Lanerolle, P. (2006) Nuclear myosin I is necessary for the formation of the first phosphodiester bond by RNA polymerase II. J. Cell. Biochem. 99: 1001-1009.
Goodrich, J.A. and Kugel, J.F. (2006) Non-coding RNA regulators of RNA polymerase II transcription. Nat. Rev. Mol. Cell Biol. 87: 612-616.
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)
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.
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.
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. 10
Weaver, J.R., Kugel, J.F., 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.
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 TAFII250) J. Biol. Chem. 279: 26257-26265.
Hofmann, W.A., Stojiljkovic, L., Fuchsova, B., Vargas, G.M., Mavrommatis, E., Philimonenko, V., Kysela, K., Goodrich, J.A., Lessard, J.L., Hope, T.J., Hozak, P. and de Lanerolle, P. (2004) Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II. Nature Cell Biol. 6: 1094-1101.
Espinoza, C.A., Allen, T.A., Hieb, A. R., Kugel, J.F., and Goodrich, J.A. (2004) B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11: 822-829.
Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F. (2004) The SINE encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11: 816-821.
Kugel, J.F. and Goodrich, J.A. (2003) In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Meth. Enzymol. 370:687-701.
Ehley, J.A., Melander, C., Herman, D., Baird, E.E., Ferguson, H.A., Goodrich, J.A., Dervan, P.B., and Gottesfeld, J.M. (2002) Promoter scanning for transcription inhibition with DNA-binding polyamides. Mol. Cell. Biol. 22: 1723-1733.
Galasinski, S.C., Resing, K.A., Goodrich, J.A., and Ahn, N.G. (2002) Phosphatase inhibition leads to histone deacteylase 1/2 phosphorylation and disruption of co-repressor interactions. J. Biol. Chem. 277: 19618-19626.
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.
Kim, L.J., Seto, A.G., Nguyen, T.N., and Goodrich, J.A. (2001) Human TAFII130 is a coactivator for NFATp. Mol. Cell. Biol. 21: 3503-3513.
Goodrich, J.A. (2001) Promoters. In Encyclopedia of Genetics. Brenner, S. and Miller, J., eds. (London: Academic Press) 1549-1551.
Lively, T.N., Ferguson, H.A., Galasinski, S.K., Seto, A.G., and Goodrich, J.A. (2001) cJun binds the N terminus of human TAFII250 to derepress RNA polymerase II transcription in vitro. J. Biol. Chem. 276: 25582-25588.
Ferguson, H.A. and Goodrich, J.A. (2001) Expression and purification of recombinant human cFos/c-Jun that is highly active in DNA binding and transcriptional activation in vitro. Nucleic Acids Res. 29: E98 (6 pages)
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.
Galasinski, S.K., Lively, T.N., Grebe de Barron, A., and Goodrich, J.A. (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.
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.
Kugel, J.F. and Goodrich, J.A. (1998) Promoter escape limits the rate of transcription from the adenovirus major late promoter on negatively supercoiled templates. Proc. Natl. Acad. Sci. USA. 95:9232-9237.