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Jennifer F. Kugel, Ph.D. - Publications

Affiliations: 
2001 University of Colorado, Boulder, Boulder, CO, United States 
Area:
Biochemistry, Cell Biology, Molecular Biology
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69 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
2024 Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules. 14. PMID 38397413 DOI: 10.3390/biom14020176  0.753
2023 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. 18: e0286193. PMID 37582100 DOI: 10.1371/journal.pone.0286193  0.587
2023 Miller GM, Brant TS, Goodrich JA, Kugel JF. Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. Febs Open Bio. PMID 37572351 DOI: 10.1002/2211-5463.13693  0.517
2023 Singh A, Miller RC, Archuleta SR, Kugel JF. Evaluating two steps in transcription using a fluorescence-based electrophoretic mobility shift assay. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. PMID 36597896 DOI: 10.1002/bmb.21708  0.441
2021 Voong CK, Goodrich JA, Kugel JF. Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules. 11. PMID 34680084 DOI: 10.3390/biom11101451  0.6
2021 Rivas T, Goodrich JA, Kugel JF. The herpes simplex virus 1 protein ICP4 acts as both an activator and repressor of host genome transcription during infection. Molecular and Cellular Biology. MCB0017121. PMID 34251885 DOI: 10.1128/MCB.00171-21  0.619
2020 Ly E, Kugel JF, Goodrich JA. Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Scientific Reports. 10: 16176. PMID 32999415 DOI: 10.1038/s41598-020-73234-6  0.578
2020 Ly E, Powell AE, Goodrich JA, Kugel JF. Release of Human TFIIB from Actively Transcribing Complexes Is Triggered upon Synthesis of 7 Nt and 9 Nt RNAs. Journal of Molecular Biology. PMID 32417370 DOI: 10.1016/J.Jmb.2020.05.005  0.699
2020 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 Biology. PMID 32129700 DOI: 10.1080/15476286.2020.1737443  0.525
2019 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. The American Journal of Pathology. PMID 31381888 DOI: 10.1016/J.Ajpath.2019.06.013  0.588
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  0.749
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  0.696
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  0.709
2017 Horn AE, Kugel JF, Goodrich JA. Understanding the Mechanisms of Human RNA Polymerase II Transcription using Single Molecule Fluorescence Colocalization Biophysical Journal. 112: 211a-212a. DOI: 10.1016/J.Bpj.2016.11.1167  0.735
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  0.716
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  0.709
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  0.758
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  0.802
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  0.678
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  0.862
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  0.71
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  0.737
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  0.78
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  0.697
2014 Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 5. PMID 24406345  0.737
2014 Horn AE, Goodrich JA, Kugel JF. Single molecule studies of RNA polymerase II transcription in vitro Transcription. 5. DOI: 10.4161/trns.27608  0.75
2014 Cardiello JF, Kugel JF, Goodrich JA. A new twist on cell growth control Cell Cycle. 13: 3474-3475. DOI: 10.4161/15384101.2014.980702  0.47
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. DOI: 10.1371/journal.pone.0101015  0.636
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  0.717
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  0.706
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  0.858
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  0.737
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  0.841
2012 Heffler MA, Walters RD, Kugel JF. Using electrophoretic mobility shift assays to measure equilibrium dissociation constants: GAL4-p53 binding DNA as a model system Biochemistry and Molecular Biology Education. 40: 383-387. PMID 23166026 DOI: 10.1002/Bmb.20649  0.525
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  0.729
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  0.788
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  0.809
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  0.72
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  0.765
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, ... ... Kugel JF, et al. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 471: 325-30. PMID 21297615 DOI: 10.1038/Nature09830  0.816
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  0.697
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  0.784
2010 Goodrich JA, Kugel JF. Genome-wide insights into eukaryotic transcriptional control. Genome Biology. 11: 305. PMID 20529212 DOI: 10.1186/Gb-2010-11-6-305  0.643
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 DOI: 10.4161/Rna.7.3.11910  0.797
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  0.859
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  0.753
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  0.855
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  0.826
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  0.69
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  0.814
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  0.777
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  0.749
2008 Kugel JF. Using FRET to measure the angle at which a protein bends DNA: TBP binding a TATA box as a model system. Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology. 36: 341-6. PMID 21591217 DOI: 10.1002/Bmb.20202  0.347
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  0.863
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  0.809
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  0.694
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  0.875
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  0.775
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  0.862
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  0.769
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  0.694
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  0.759
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  0.755
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  0.857
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  0.769
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 DOI: 10.1128/Mcb.22.3.762-773.2002  0.804
2001 Ferguson HA, Kugel JF, Goodrich JA. Kinetic and mechanistic analysis of the RNA polymerase II transcription reaction at the human interleukin-2 promoter Journal of Molecular Biology. 314: 993-1006. PMID 11743717 DOI: 10.1006/Jmbi.2000.5215  0.733
2000 Kugel JF, Goodrich JA. A kinetic model for the early steps of RNA synthesis by human RNA polymerase II Journal of Biological Chemistry. 275: 40483-40491. PMID 10982810 DOI: 10.1074/Jbc.M006401200  0.789
1998 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 Proceedings of the National Academy of Sciences of the United States of America. 95: 9232-9237. PMID 9689063 DOI: 10.1073/Pnas.95.16.9232  0.773
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