James A. Goodrich - Publications

Affiliations: 
University of Colorado, Boulder, Boulder, CO, United States 
Area:
Biochemistry

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ly E, Goodrich JA, Kugel JF. Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization. Methods (San Diego, Calif.). PMID 30876965 DOI: 10.1016/j.ymeth.2019.03.006  1
2018 Cardiello JF, Goodrich JA, Kugel JF. Heat shock causes a reversible increase in RNA polymerase II occupancy downstream of mRNA genes consistent with a global loss in transcriptional termination. Molecular and Cellular Biology. PMID 29967245 DOI: 10.1128/MCB.00181-18  1
2017 Kugel JF, Goodrich JA. Finding the start site: redefining the human initiator element. Genes & Development. 31: 1-2. PMID 28130343 DOI: 10.1101/gad.295980.117  1
2016 Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Correction for Abrisch et al., Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. Journal of Virology. 90: 11279. PMID 27895185 DOI: 10.1128/JVI.01903-16  1
2016 Blair RH, Horn AE, Pazhani Y, Grado L, Goodrich JA, Kugel JF. The HMGB1 C-terminal tail regulates DNA bending. Journal of Molecular Biology. PMID 27558111 DOI: 10.1016/j.jmb.2016.08.018  1
2016 Horn AE, Kugel JF, Goodrich JA. Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity. Nucleic Acids Research. PMID 27112574 DOI: 10.1093/nar/gkw321  1
2016 Eidem TM, Kugel JF, Goodrich JA. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. Journal of Molecular Biology. PMID 26920110 DOI: 10.1016/j.jmb.2016.02.019  1
2015 Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Infection by Herpes Simplex Virus Type-1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. Journal of Virology. PMID 26676778 DOI: 10.1128/JVI.02665-15  1
2015 Ponicsan SL, Kugel JF, Goodrich JA. 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. PMID 26405685 DOI: 10.3390/ncrna1010004  1
2015 Goodrich JA, Kugel JF. Studying the affinity, kinetic stability, and specificity of RNA/protein interactions: SINE ncRNA/Pol II complexes as a model system Methods in Molecular Biology. 1206: 165-178. PMID 25240896 DOI: 10.1007/978-1-4939-1369-5_15  1
2014 Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 5: e27608. PMID 25764112 DOI: 10.4161/trns.27608  1
2014 Cardiello JF, Kugel JF, Goodrich JA. A new twist on cell growth control. Cell Cycle (Georgetown, Tex.). 13: 3474-5. PMID 25493414 DOI: 10.4161/15384101.2014.980702  1
2014 Walters RD, McSwiggen DT, Goodrich JA, Kugel JF. Selection and characterization of a DNA aptamer that can discriminate between cJun/cJun and cJun/cFos. Plos One. 9: e101015. PMID 24968026 DOI: 10.1371/journal.pone.0101015  1
2014 Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 5. PMID 24406345  1
2013 Walters RD, Drullinger LF, Kugel JF, Goodrich JA. NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription Molecular Immunology. 56: 48-56. PMID 23665382 DOI: 10.1016/j.molimm.2013.03.022  1
2013 Blair RH, Goodrich JA, Kugel JF. Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system. Methods in Molecular Biology (Clifton, N.J.). 977: 203-15. PMID 23436364 DOI: 10.1007/978-1-62703-284-1_16  1
2013 Ponicsan SL, Houel S, Old WM, Ahn NG, Goodrich JA, Kugel JF. The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II Journal of Molecular Biology. 425: 3625-3638. PMID 23416138 DOI: 10.1016/j.jmb.2013.01.035  1
2013 Kugel JF, Goodrich JA. The regulation of mammalian mRNA transcription by lncRNAs: Recent discoveries and current concepts Epigenomics. 5: 95-102. PMID 23414324 DOI: 10.2217/epi.12.69  1
2013 Wagner SD, Yakovchuk P, Gilman B, Ponicsan SL, Drullinger LF, Kugel JF, Goodrich JA. RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. The Embo Journal. 32: 781-90. PMID 23395899 DOI: 10.1038/emboj.2013.18  1
2013 Kassube SA, Fang J, Grob P, Yakovchuk P, Goodrich JA, Nogales E. Structural insights into transcriptional repression by noncoding RNAs that bind to human Pol II. Journal of Molecular Biology. 425: 3639-48. PMID 22954660 DOI: 10.1016/j.jmb.2012.08.024  1
2012 Blair RH, Goodrich JA, Kugel JF. Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics. Biochemistry. 51: 7444-55. PMID 22934924 DOI: 10.1021/bi300491j  1
2012 Dridi S, Hirano Y, Tarallo V, Kim Y, Fowler BJ, Ambati BK, Bogdanovich S, Chiodo VA, Hauswirth WW, Kugel JF, Goodrich JA, Ponicsan SL, Hinton DR, Kleinman ME, Baffi JZ, et al. ERK1/2 activation is a therapeutic target in age-related macular degeneration. Proceedings of the National Academy of Sciences of the United States of America. 109: 13781-6. PMID 22869729 DOI: 10.1073/pnas.1206494109  1
2012 Tarallo V, Hirano Y, Gelfand BD, Dridi S, Kerur N, Kim Y, Cho WG, Kaneko H, Fowler BJ, Bogdanovich S, Albuquerque RJ, Hauswirth WW, Chiodo VA, Kugel JF, Goodrich JA, et al. DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell. 149: 847-59. PMID 22541070 DOI: 10.1016/j.cell.2012.03.036  1
2012 Kugel JF, Goodrich JA. Non-coding RNAs: Key regulators of mammalian transcription Trends in Biochemical Sciences. 37: 144-151. PMID 22300815 DOI: 10.1016/j.tibs.2011.12.003  1
2011 Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA represses TFIIH phosphorylation of RNA polymerase II Transcription. 2: 45-49. PMID 21326911 DOI: 10.4161/trns.2.1.14306  1
2011 Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Karikó K, Yoo JW, Lee DK, Hadziahmetovic M, Song Y, ... ... Goodrich JA, et al. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 471: 325-30. PMID 21297615 DOI: 10.1038/nature09830  1
2011 Titov DV, Gilman B, He QL, Bhat S, Low WK, Dang Y, Smeaton M, Demain AL, Miller PS, Kugel JF, Goodrich JA, Liu JO. XPB, a subunit of TFIIH, is a target of the natural product triptolide. Nature Chemical Biology. 7: 182-8. PMID 21278739 DOI: 10.1038/nchembio.522  1
2010 Goodrich JA, Tjian R. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nature Reviews. Genetics. 11: 549-58. PMID 20628347 DOI: 10.1038/nrg2847  1
2010 Nguyen TN, Kim LJ, Walters RD, Drullinger LF, Lively TN, Kugel JF, Goodrich JA. The C-terminal region of human NFATc2 binds cJun to synergistically activate interleukin-2 transcription Molecular Immunology. 47: 2314-2322. PMID 20557936 DOI: 10.1016/j.molimm.2010.05.287  1
2010 Goodrich JA, Kugel JF. Genome-wide insights into eukaryotic transcriptional control. Genome Biology. 11: 305. PMID 20529212  1
2010 Goodrich JA, Kugel JF. Dampening DNA binding: A common mechanism of transcriptional repression for both ncRNAs and protein domains Rna Biology. 7. PMID 20436282  1
2010 Ponicsan SL, Kugel JF, Goodrich JA. Genomic gems: SINE RNAs regulate mRNA production Current Opinion in Genetics and Development. 20: 149-155. PMID 20176473 DOI: 10.1016/j.gde.2010.01.004  1
2010 Yakovchuk P, Gilman B, Goodrich JA, Kugel JF. RNA Polymerase II and TAFs Undergo a Slow Isomerization after the Polymerase Is Recruited to Promoter-Bound TFIID Journal of Molecular Biology. 397: 57-68. PMID 20083121 DOI: 10.1016/j.jmb.2010.01.025  1
2010 Wagner SD, Kugel JF, Goodrich JA. TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain Molecular and Cellular Biology. 30: 91-97. PMID 19841064 DOI: 10.1128/MCB.01115-09  1
2009 Walters RD, Kugel JF, Goodrich JA. InvAluable junk: The cellular impact and function of Alu and B2 RNAs Iubmb Life. 61: 831-837. PMID 19621349 DOI: 10.1002/iub.227  1
2009 Kugel JF, Goodrich JA. In new company: U1 snRNA associates with TAF15 Embo Reports. 10: 454-456. PMID 19373252 DOI: 10.1038/embor.2009.65  1
2009 Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes Proceedings of the National Academy of Sciences of the United States of America. 106: 5569-5574. PMID 19307572 DOI: 10.1073/pnas.0810738106  1
2009 Gilman B, Drullinger LF, Kugel JF, Goodrich JA. TATA-binding protein and transcription factor IIB induce transcript slipping during early transcription by RNA polymerase II Journal of Biological Chemistry. 284: 9093-9098. PMID 19193635 DOI: 10.1074/jbc.M900019200  1
2009 Goodrich JA, Kugel JF. From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription roles of noncoding RNAs in regulating transcription J. A. Goodrich and J. F. Kugel Critical Reviews in Biochemistry and Molecular Biology. 44: 3-15. PMID 19107624 DOI: 10.1080/10409230802593995  1
2008 Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock Molecular Cell. 29: 499-509. PMID 18313387 DOI: 10.1016/j.molcel.2007.12.013  1
2007 Hieb AR, Halsey WA, Betterton MD, Perkins TT, Kugel JF, Goodrich JA. TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. Journal of Molecular Biology. 372: 619-32. PMID 17681538 DOI: 10.1016/j.jmb.2007.06.061  1
2007 Weaver JR, Good K, Walters RD, Kugel JF, Goodrich JA. Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter Molecular Immunology. 44: 2813-2819. PMID 17337059 DOI: 10.1016/j.molimm.2007.01.027  1
2007 Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription Rna. 13: 583-596. PMID 17307818 DOI: 10.1261/rna.310307  1
2007 Kugel JF, Goodrich JA. An RNA transcriptional regulator templates its own regulatory RNA Nature Chemical Biology. 3: 89-90. PMID 17235345 DOI: 10.1038/nchembio0207-89  1
2006 Hieb AR, Baran S, Goodrich JA, Kugel JF. An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation Embo Journal. 25: 3100-3109. PMID 16778763 DOI: 10.1038/sj.emboj.7601197  1
2006 Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription Nature Reviews Molecular Cell Biology. 7: 612-616. PMID 16723972 DOI: 10.1038/nrm1946  1
2006 Kugel JF, Goodrich JA. Beating the Heat: A Translation Factor and an RNA Mobilize the Heat Shock Transcription Factor HSF1 Molecular Cell. 22: 153-154. PMID 16630884 DOI: 10.1016/j.molcel.2006.04.003  1
2006 Nguyen TN, Goodrich JA. Protein-protein interaction assays: eliminating false positive interactions. Nature Methods. 3: 135-9. PMID 16432524 DOI: 10.1038/nmeth0206-135  1
2005 Weaver JR, Kugel JF, Goodrich JA. The sequence at specific positions in the early transcribed region sets the rate of transcript synthesis by RNA polymerase II in vitro Journal of Biological Chemistry. 280: 39860-39869. PMID 16210313 DOI: 10.1074/jbc.M509376200  1
2004 Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature Structural & Molecular Biology. 11: 816-21. PMID 15300240 DOI: 10.1038/nsmb813  1
2004 Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature Structural & Molecular Biology. 11: 822-9. PMID 15300239 DOI: 10.1038/nsmb812  1
2004 Lively TN, Nguyen TN, Galasinski SK, Goodrich JA. The basic leucine zipper domain of c-Jun functions in transcriptional activation through interaction with the N terminus of human TATA-binding protein-associated factor-1 (human TAF(II)250). The Journal of Biological Chemistry. 279: 26257-65. PMID 15087451 DOI: 10.1074/jbc.M400892200  1
2003 Kugel JF, Goodrich JA. In Vitro Studies of the Early Steps of RNA Synthesis by Human RNA Polymerase II Methods in Enzymology. 370: 687-701. PMID 14712684 DOI: 10.1016/S0076-6879(03)70056-1  1
2002 Galasinski SC, Resing KA, Goodrich JA, Ahn NG. Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions. The Journal of Biological Chemistry. 277: 19618-26. PMID 11919195 DOI: 10.1074/jbc.M201174200  0.4
2002 Ehley JA, Melander C, Herman D, Baird EE, Ferguson HA, Goodrich JA, Dervan PB, Gottesfeld JM. Promoter scanning for transcription inhibition with DNA-binding polyamides. Molecular and Cellular Biology. 22: 1723-33. PMID 11865052 DOI: 10.1128/MCB.22.6.1723-1733.2002  1
2002 Kugel JF, Goodrich JA. Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape Molecular and Cellular Biology. 22: 762-773. PMID 11784853  1
2001 Lively TN, Ferguson HA, Galasinski SK, Seto AG, Goodrich JA. c-Jun binds the N terminus of human TAF(II)250 to derepress RNA polymerase II transcription in vitro. The Journal of Biological Chemistry. 276: 25582-8. PMID 11316804 DOI: 10.1074/jbc.M100278200  1
2001 Kim LJ, Seto AG, Nguyen TN, Goodrich JA. Human Taf(II)130 is a coactivator for NFATp. Molecular and Cellular Biology. 21: 3503-13. PMID 11313476 DOI: 10.1128/MCB.21.10.3503-3513.2001  1
2000 Kim LJ, Ferguson HA, Seto AG, Goodrich JA. Characterization of DNA binding, transcriptional activation, and regulated nuclear association of recombinant human NFATp. Bmc Immunology. 1: 1. PMID 11231878 DOI: 10.1186/1471-2172-1-1  1
2000 Galasinski SK, Lively TN, Grebe De Barron A, Goodrich JA. Acetyl coenzyme A stimulates RNA polymerase II transcription and promoter binding by transcription factor IID in the absence of histones. Molecular and Cellular Biology. 20: 1923-30. PMID 10688640 DOI: 10.1128/MCB.20.6.1923-1930.2000  1
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