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James Andrew Goodrich

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentChemistry & Biochemistry
Phone303/492-3273
ORCID ORCID Icon0000-0002-5754-8427 Additional info

    Collapse Research 
    Collapse research activities and funding
    R01GM055235     (GOODRICH, JAMES)Aug 1, 1998 - Nov 30, 2012
    NIH/NIGMS
    Regulation of Transcription at the Human IL-2 Promoter
    Role: Principal Investigator

    R01GM068414     (GOODRICH, JAMES)Sep 19, 2003 - Aug 31, 2019
    NIH/NIGMS
    Regulation of RNA Metabolism by the RNA-dependent RNA Polymerase Activity of Mammalian RNA polymerase II
    Role: Principal Investigator

    R13CA119826     (GOODRICH, JAMES)Apr 14, 2006 - Mar 31, 2007
    NIH/NCI
    Regulation of Eukaryotic Transcription:Chromatin to mRNA
    Role: Principal Investigator

    R03AI101193     (GOODRICH, JAMES)Dec 21, 2012 - Nov 30, 2015
    NIH/NIAID
    Do the B2 and Alu ncRNAs Repress Host Cell mRNA Transcription During HSV-1 Infect
    Role: Principal Investigator

    R03ES023134     (GOODRICH, JAMES)Jul 25, 2013 - Jun 30, 2015
    NIH/NIEHS
    Do NFATc2 and cJun Cooperate to Activate Transcription in Breast Cancer Cells?
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Kugel JF, Goodrich JA. Finding the start site: redefining the human initiator element. Genes Dev. 2017 Jan 01; 31(1):1-2. PMID: 28130343.
      View in: PubMed
    2. 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. J Virol. 2016 Dec 15; 90(24):11279. PMID: 27895185.
      View in: PubMed
    3. Blair RH, Horn AE, Pazhani Y, Grado L, Goodrich JA, Kugel JF. The HMGB1 C-Terminal Tail Regulates DNA Bending. J Mol Biol. 2016 Oct 09; 428(20):4060-4072. PMID: 27558111.
      View in: PubMed
    4. Horn AE, Kugel JF, Goodrich JA. Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity. Nucleic Acids Res. 2016 Sep 06; 44(15):7132-43. PMID: 27112574; PMCID: PMC5009721.
    5. Eidem TM, Kugel JF, Goodrich JA. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. J Mol Biol. 2016 Jun 19; 428(12):2652-9. PMID: 26920110; PMCID: PMC4894004 [Available on 06/19/17].
    6. Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA. Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. J Virol. 2015 Dec 16; 90(5):2503-13. PMID: 26676778; PMCID: PMC4810688.
    7. 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. Noncoding RNA. 2015 Jun; 1:4-16. PMID: 26405685.
      View in: PubMed
    8. 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 Mol Biol. 2015; 1206:165-78. PMID: 25240896; PMCID: PMC4591035.
    9. 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. 2014; 9(6):e101015. PMID: 24968026; PMCID: PMC4072727.
    10. Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 2014 Jan 08; 5(1). PMID: 24406345.
      View in: PubMed
    11. Cardiello JF, Kugel JF, Goodrich JA. A new twist on cell growth control. Cell Cycle. 2014; 13(22):3474-5. PMID: 25493414; PMCID: PMC4614046.
    12. Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 2014; 5(1):e27608. PMID: 25764112; PMCID: PMC4214229.
    13. Walters RD, Drullinger LF, Kugel JF, Goodrich JA. NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription. Mol Immunol. 2013 Nov; 56(1-2):48-56. PMID: 23665382; PMCID: PMC3686915.
    14. 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. J Mol Biol. 2013 Oct 09; 425(19):3625-38. PMID: 23416138; PMCID: PMC3672349.
    15. 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. EMBO J. 2013 Mar 20; 32(6):781-90. PMID: 23395899; PMCID: PMC3604716.
    16. Kugel JF, Goodrich JA. The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts. Epigenomics. 2013 Feb; 5(1):95-102. PMID: 23414324; PMCID: PMC3702037.
    17. Blair RH, Goodrich JA, Kugel JF. Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system. Methods Mol Biol. 2013; 977:203-15. PMID: 23436364.
      View in: PubMed
    18. 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. 2012 Sep 25; 51(38):7444-55. PMID: 22934924; PMCID: PMC3551999.
    19. Kugel JF, Goodrich JA. Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci. 2012 Apr; 37(4):144-51. PMID: 22300815; PMCID: PMC3323709.
    20. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription. 2011 Jan-Feb; 2(1):45-9. PMID: 21326911; PMCID: PMC3023648.
    21. Goodrich JA, Tjian R. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet. 2010 Aug; 11(8):549-58. PMID: 20628347; PMCID: PMC2965628.
    22. 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. Mol Immunol. 2010 Aug; 47(14):2314-22. PMID: 20557936; PMCID: PMC2918688.
    23. Goodrich JA, Kugel JF. Genome-wide insights into eukaryotic transcriptional control. Genome Biol. 2010; 11(6):305. PMID: 20529212; PMCID: PMC2911103.
    24. Goodrich JA, Kugel JF. Dampening DNA binding: a common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biol. 2010 May-Jun; 7(3):305-9. PMID: 20436282; PMCID: PMC2964417.
    25. Ponicsan SL, Kugel JF, Goodrich JA. Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev. 2010 Apr; 20(2):149-55. PMID: 20176473; PMCID: PMC2859989.
    26. 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. J Mol Biol. 2010 Mar 19; 397(1):57-68. PMID: 20083121.
      View in: PubMed
    27. Wagner SD, Kugel JF, Goodrich JA. TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain. Mol Cell Biol. 2010 Jan; 30(1):91-7. PMID: 19841064; PMCID: PMC2798307.
    28. Walters RD, Kugel JF, Goodrich JA. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life. 2009 Aug; 61(8):831-7. PMID: 19621349; PMCID: PMC4049031.
    29. Kugel JF, Goodrich JA. In new company: U1 snRNA associates with TAF15. EMBO Rep. 2009 May; 10(5):454-6. PMID: 19373252; PMCID: PMC2680880.
    30. 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. Proc Natl Acad Sci U S A. 2009 Apr 07; 106(14):5569-74. PMID: 19307572; PMCID: PMC2667051.
    31. 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. J Biol Chem. 2009 Apr 03; 284(14):9093-8. PMID: 19193635; PMCID: PMC2666558.
    32. Goodrich JA, Kugel JF. 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. 2009 Jan-Feb; 44(1):3-15. PMID: 19107624; PMCID: PMC2659850.
    33. 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. Mol Cell. 2008 Feb 29; 29(4):499-509. PMID: 18313387.
      View in: PubMed
    34. 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. J Mol Biol. 2007 Sep 21; 372(3):619-32. PMID: 17681538.
      View in: PubMed
    35. 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. Mol Immunol. 2007 Apr; 44(11):2813-9. PMID: 17337059; PMCID: PMC1924494.
    36. 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. 2007 Apr; 13(4):583-96. PMID: 17307818; PMCID: PMC1831867.
    37. 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 J. 2006 Jul 12; 25(13):3100-9. PMID: 16778763; PMCID: PMC1500975.
    38. Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol. 2006 Aug; 7(8):612-6. PMID: 16723972.
      View in: PubMed
    39. Kugel JF, Goodrich JA. Beating the heat: A translation factor and an RNA mobilize the heat shock transcription factor HSF1. Mol Cell. 2006 Apr 21; 22(2):153-4. PMID: 16630884.
      View in: PubMed
    40. Nguyen TN, Goodrich JA. Protein-protein interaction assays: eliminating false positive interactions. Nat Methods. 2006 Feb; 3(2):135-9. PMID: 16432524; PMCID: PMC2730730.
    41. 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. J Biol Chem. 2005 Dec 02; 280(48):39860-9. PMID: 16210313.
      View in: PubMed
    42. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol. 2004 Sep; 11(9):816-21. PMID: 15300240.
      View in: PubMed
    43. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol. 2004 Sep; 11(9):822-9. PMID: 15300239.
      View in: PubMed
    44. 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). J Biol Chem. 2004 Jun 18; 279(25):26257-65. PMID: 15087451.
      View in: PubMed
    45. Kugel JF, Goodrich JA. In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Methods Enzymol. 2003; 370:687-701. PMID: 14712684.
      View in: PubMed
    46. Galasinski SC, Resing KA, Goodrich JA, Ahn NG. Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions. J Biol Chem. 2002 May 31; 277(22):19618-26. PMID: 11919195.
      View in: PubMed
    47. Kugel JF, Goodrich JA. Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape. Mol Cell Biol. 2002 Feb; 22(3):762-73. PMID: 11784853; PMCID: PMC133543.
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