Research Publications:

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Walters, R.D., Drullinger, L.F., Kugel, J.F., Goodrich, J.A. (2013). NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription. Mol Immunol. 56: 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. Epub ahead of print.

Wagner, S.D., Yakovchuk, P., Gilman, B., Poniscan, S.L., Drullinger, L.F., Kugel, J.F., 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. Epub ahead of print.

Kassube, S.A., Fang, J., Grob, P., Yakovchuk, P., Goodrich, J.A., Nogales, E. (2012). Structural insights into transcriptional repression by ncRNAs that bind to human Pol II. J. Mol. Biol. Epub ahead of print.

Blair, R.H. Goodrich, J.A., and Kugel, J.F. (2012). Single molecule FRET shows uniformity in TBP-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., Kim, Y., Kerur, N., 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., Dunaief, J., Ambati, B.K., Ogura, Y., Yoo, J.W., Lee, D.-K., Provost, P., Hinton, D.R., N˙˝ez, 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.

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., Karikˇ, 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 deficit induces Alu RNA toxicity 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. Nature Chemical Biology. 7:182-188. PMID: 21278739

Yakovchuk, P., Goodrich, J.A., Kugel, J.F. (2011) B2 RNA represses TFIIH phosphorylation of RNA polymerase II.. Transcription. Jan;2(1):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(14):2314-22

Yakovchuk, P., Gilman B., Goodrich, J.A., 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(1):57-68

Wagner, S.D., Kugel, J.F., Goodrich, J.A. (2010) TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain.. Mol Cell Biol.30(1):91-7

Yakovchuk, P., Goodrich, J.A., 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 U S A. 106(14):5569-74

Gilman, B., Drullinger, L.F., Kugel, J.F., 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(14):9093-8.

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.

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 promoterMol. Immunol.  44: 2813-2819.

Hieb A.R., Halsey W.A., Betterton M.D., Perkins T.T., Kugel J.F., Goodrich J.A. (2007) TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. J Mol Biol. 21;372(3):619-32.

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 transcriptionRNA.  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 elongationEMBO 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 vitroJ. 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:

Goodrich J.A., Tjian, R. (2011) Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet. (8):549-58

Goodrich J.A., and Kugel J.F.(2010) Genome-wide insights into eukaryotic transcriptional control Genome Biol(6):305

Kugel J.F., and Goodrich J.A.(2010) Dampening DNA binding: a common mechanism of transcriptional repression for both ncRNAs and protein domains RNA Bio(3):305-9

Ponicsan S.L., Kugel J.F., and Goodrich J.A., (2010) Genomic gems: SINE RNAs regulate mRNA production Curr Opin Genet Dev(2):149-55

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(8):831-7

Goodrich J.A., 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(1):3-15.

Wagner, S.D., Goodrich, J.A. and Kugel, J.F. (2008). RNA and the Regulation of Gene Expression; Chapter 9: The Role of Non-Coding RNAs in Controlling Mammalian RNA Polymerase II Transcription. Caister Academic Press.

Kugel, J.F. and Goodrich, J.A.  (2007).  An RNA transcriptional regulator templates its own regulatory RNANature Chem. Biol.  3: 89-90.

Goodrich, J.A. and Kugel, J.F.  (2006).  Noncoding RNA regulators of RNA polymerase II transcriptionNature 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 HSF1Mol. 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 acidNature 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 IIMethods 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/.