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Jennifer Franzen Kugel

TitleProfessor-Research
InstitutionUniversity of Colorado Boulder
DepartmentBiochemistry
Phone303/492-3596

    Collapse Research 
    Collapse research activities and funding
    R01GM148613     (KUGEL, JENNIFER F.)Mar 10, 2023 - Jan 31, 2027
    NIH
    Unraveling the biological roles of specific miRNAs, from experimental target identification through functional characterization
    Role: Principal Investigator
    R03AA026386     (KUGEL, JENNIFER F.)Aug 10, 2018 - Jul 31, 2021
    NIH
    Defining the Genome-wide Alcohol-induced Transcriptional Changes in Breast Cancer
    Role: Principal Investigator
    R21AR067826     (KUGEL, JENNIFER F.)Apr 1, 2015 - Mar 31, 2018
    NIH
    Identify the Transcriptome and Proteome Associated with miRNAs dring Myogenesis
    Role: Principal Investigator
    R21AI079374     (KUGEL, JENNIFER F.)Jun 15, 2008 - May 31, 2011
    NIH
    Controlling NFAT1 in T cells using engineered ncRNA transcriptional regulators
    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.
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    1. Miller GM, Brant TS, Goodrich JA, Kugel JF. Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. FEBS Open Bio. 2023 10; 13(10):1941-1952. PMID: 37572351.
      View in: PubMed
    2. Suwita JP, Voong CK, Ly E, Goodrich JA, Kugel JF. Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements. PLoS One. 2023; 18(8):e0286193. PMID: 37582100.
      View in: PubMed
    3. Scott AK, Casas E, Schneider SE, Swearingen AR, Van Den Elzen CL, Seelbinder B, Barthold JE, Kugel JF, Stern JL, Foster KJ, Emery NC, Brumbaugh J, Neu CP. Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophys J. 2023 04 18; 122(8):1428-1444. PMID: 36871159.
      View in: PubMed
    4. Singh A, Miller RC, Archuleta SR, Kugel JF. Evaluating two steps in transcription using a fluorescence-based electrophoretic mobility shift assay. Biochem Mol Biol Educ. 2023 03; 51(2):230-235. PMID: 36597896.
      View in: PubMed
    5. Bosire R, Fadel L, Mocs?r G, N?n?si P, Sen P, Sharma AK, Naseem MU, Kov?cs A, Kugel J, Kroemer G, V?mosi G, Szab? G. Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Sci Rep. 2022 05 16; 12(1):8087. PMID: 35577872.
      View in: PubMed
    6. Voong CK, Goodrich JA, Kugel JF. Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules. 2021 10 02; 11(10). PMID: 34680084.
      View in: PubMed
    7. Rivas T, Goodrich JA, Kugel JF. The Herpes Simplex Virus 1 Protein ICP4 Acts as both an Activator and a Repressor of Host Genome Transcription during Infection. Mol Cell Biol. 2021 09 24; 41(10):e0017121. PMID: 34251885.
      View in: PubMed
    8. Ly E, Kugel JF, Goodrich JA. Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Sci Rep. 2020 09 30; 10(1):16176. PMID: 32999415.
      View in: PubMed
    9. Ly E, Powell AE, Goodrich JA, Kugel JF. Release of Human TFIIB from Actively Transcribing Complexes Is Triggered upon Synthesis of 7- and 9-nt RNAs. J Mol Biol. 2020 06 26; 432(14):4049-4060. PMID: 32417370.
      View in: PubMed
    10. Salant GM, Tat KL, Goodrich JA, Kugel JF. miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs. RNA Biol. 2020 07; 17(7):956-965. PMID: 32129700.
      View in: PubMed
    11. Greene E, Flees J, Dhamad A, Alrubaye A, Hennigan S, Pleimann J, Smeltzer M, Murray S, Kugel J, Goodrich J, Robertson A, Wideman R, Rhoads D, Dridi S. Double-Stranded RNA Is a Novel Molecular Target in Osteomyelitis Pathogenesis: A Translational Avian Model for Human Bacterial Chondronecrosis with Osteomyelitis. Am J Pathol. 2019 10; 189(10):2077-2089. PMID: 31381888.
      View in: PubMed
    12. Ly E, Goodrich JA, Kugel JF. Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization. Methods. 2019 04 15; 159-160:45-50. PMID: 30876965.
      View in: PubMed
    13. 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. Mol Cell Biol. 2018 09 15; 38(18). PMID: 29967245.
      View in: PubMed
    14. Kugel JF, Goodrich JA. Finding the start site: redefining the human initiator element. Genes Dev. 2017 01 01; 31(1):1-2. PMID: 28130343.
      View in: PubMed
    15. 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 12 15; 90(24):11279. PMID: 27895185.
      View in: PubMed
    16. Blair RH, Horn AE, Pazhani Y, Grado L, Goodrich JA, Kugel JF. The HMGB1 C-Terminal Tail Regulates DNA Bending. J Mol Biol. 2016 10 09; 428(20):4060-4072. PMID: 27558111.
      View in: PubMed
    17. 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 09 06; 44(15):7132-43. PMID: 27112574.
      View in: PubMed
    18. Eidem TM, Kugel JF, Goodrich JA. Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. J Mol Biol. 2016 06 19; 428(12):2652-2659. PMID: 26920110.
      View in: PubMed
    19. 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 12 16; 90(5):2503-13. PMID: 26676778.
      View in: PubMed
    20. 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
    21. 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.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. Cardiello JF, Kugel JF, Goodrich JA. A new twist on cell growth control. Cell Cycle. 2014; 13(22):3474-5. PMID: 25493414.
      View in: PubMed
    24. Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 2014; 5(1):e27608. PMID: 25764112.
      View in: PubMed
    25. 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.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. 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
    30. Heffler MA, Walters RD, Kugel JF. Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4-p53 binding DNA as a model system. Biochem Mol Biol Educ. 2012 Nov-Dec; 40(6):383-7. PMID: 23166026.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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, Gelfand BD, Ambati J. ERK1/2 activation is a therapeutic target in age-related macular degeneration. Proc Natl Acad Sci U S A. 2012 Aug 21; 109(34):13781-6. PMID: 22869729.
      View in: PubMed
    33. 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, Ponicsan SL, Chaudhuri G, Murphy MP, Dunaief JL, Ambati BK, Ogura Y, Yoo JW, Lee DK, Provost P, Hinton DR, N??ez G, Baffi JZ, Kleinman ME, Ambati J. DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell. 2012 May 11; 149(4):847-59. PMID: 22541070.
      View in: PubMed
    34. Kugel JF, Goodrich JA. Non-coding RNAs: key regulators of mammalian transcription. Trends Biochem Sci. 2012 Apr; 37(4):144-51. PMID: 22300815.
      View in: PubMed
    35. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Karik? K, Yoo JW, Lee DK, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJ, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MM, Provost P, Kugel JF, Goodrich JA, Dunaief JL, Baffi JZ, Ambati J. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 2011 Mar 17; 471(7338):325-30. PMID: 21297615.
      View in: PubMed
    36. 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. Nat Chem Biol. 2011 Mar; 7(3):182-8. PMID: 21278739.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. 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.
      View in: PubMed
    39. Goodrich JA, Kugel JF. Genome-wide insights into eukaryotic transcriptional control. Genome Biol. 2010; 11(6):305. PMID: 20529212.
      View in: PubMed
    40. 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.
      View in: PubMed
    41. 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.
      View in: PubMed
    42. 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
    43. 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.
      View in: PubMed
    44. 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.
      View in: PubMed
    45. Kugel JF, Goodrich JA. In new company: U1 snRNA associates with TAF15. EMBO Rep. 2009 May; 10(5):454-6. PMID: 19373252.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. 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.
      View in: PubMed
    48. 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.
      View in: PubMed
    49. Kugel JF. Using FRET to measure the angle at which a protein bends DNA: TBP binding a TATA box as a model system. Biochem Mol Biol Educ. 2008 Sep; 36(5):341-6. PMID: 21591217.
      View in: PubMed
    50. 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
    51. 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
    52. 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.
      View in: PubMed
    53. 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.
      View in: PubMed
    54. Kugel JF, Goodrich JA. An RNA transcriptional regulator templates its own regulatory RNA. Nat Chem Biol. 2007 Feb; 3(2):89-90. PMID: 17235345.
      View in: PubMed
    55. 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.
      View in: PubMed
    56. 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
    57. 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
    58. 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
    59. 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
    60. 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
    61. 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
    62. 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.
      View in: PubMed
    63. Ferguson HA, Kugel JF, Goodrich JA. Kinetic and mechanistic analysis of the RNA polymerase II transcrption reaction at the human interleukin-2 promoter. J Mol Biol. 2001 Dec 14; 314(5):993-1006. PMID: 11743717.
      View in: PubMed
    64. Kugel JF, Goodrich JA. A kinetic model for the early steps of RNA synthesis by human RNA polymerase II. J Biol Chem. 2000 Dec 22; 275(51):40483-91. PMID: 10982810.
      View in: PubMed
    65. Kugel JF, Goodrich JA. Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA. Proc Natl Acad Sci U S A. 1998 Aug 04; 95(16):9232-7. PMID: 9689063.
      View in: PubMed
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