Publications in VIVO

Co-author Network

Goodrich, Jim

Professor

Positions

Professor, Biochemistry
Chair, Biochemistry

Research Areas

Research

keywords

mechanisms of mammalian RNA polymerase II transcription, non-coding RNA regulators of RNA polymerase II, SINE encoded RNAs, single molecule FRET studies of transcription complexes

Publications

selected publications

book
- Binding and Kinetics for Molecular Biologists 2007
chapter
- Transcription: The never ending story 2013
- The role of non-coding RNAs in controlling mammalian RNA polymerase II transcription 2008
conference proceeding
- Understanding the Mechanisms of Human RNA Polymerase II Transcription using Single Molecule Fluorescence Colocalization. Biophysical Journal. 211A-212A. 2014
- Human TBP Bending of DNA Measured at the Single Molecule Level. Biophysical Journal. 57A-57A. 2009
- Transcriptional repression by non-coding RNA regulators of the mammalian heat shock response. The FASEB Journal. 2008
- An apparent motor function for nuclear myosin I and beta-actin in transcription.. Biophysical Journal. 410A-410A. 2002
journal article
- Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules. 2024
- Short-term exposure to ethanol induces transcriptional changes in nontumorigenic breast cells. FEBS Open Bio. 1941-1952. 2023
- Single molecule studies characterize the kinetic mechanism of tetrameric p53 binding to different native response elements. PLoS One. 2023
- Multiple RNA- and DNA- binding proteins exhibit direct transfer of polynucleotides with implications for target- site search. Proceedings of the National Academy of Sciences of USA. 2023
- Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules. 2021
- The Herpes Simplex Virus 1 Protein ICP4 Acts as both an Activator and a Repressor of Host Genome Transcription during Infection. Molecular and Cellular Biology. 2021
- Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites. Scientific Reports. 2020
- miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs. RNA Biology. 956-965. 2020
- Release of Human TFIIB from Actively Transcribing Complexes Is Triggered upon Synthesis of 7-and 9-nt RNAs. Journal of Molecular Biology. 4049-4060. 2020
- Double-Stranded RNA Is a Novel Molecular Target in Osteomyelitis Pathogenesis A Translational Avian Model for Human Bacterial Chondronecrosis with Osteomyelitis. American Journal of Pathology. 2077-2089. 2019
- Monitoring transcriptional activity by RNA polymerase II in vitro using single molecule co-localization. Methods. 45-50. 2019
- 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. 2018
- A new phase in transcription. Nature. 197-198. 2018
- Finding the start site: redefining the human initiator element. Genes and Development. 1-2. 2017
- Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome (vol 90, pg 2503, 2016). Journal of Virology. 11279-11279. 2016
- The HMGB1 C-Terminal Tail Regulates DNA Bending. Journal of Molecular Biology. 4060-4072. 2016
- Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity. Nucleic Acids Research. 7132-7143. 2016
- Noncoding RNAs: Regulators of the Mammalian Transcription Machinery. Journal of Molecular Biology. 2652-2659. 2016
- Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. Journal of Virology. 2503-2513. 2016
- Repression of RNA Polymerase II Transcription by B2 RNA Depends on a Specific Pattern of Structural Regions in the RNA.. Non-Coding RNA. 4-16. 2015
- Studying the Affinity, Kinetic Stability, and Specificity of RNA/Protein Interactions: SINE ncRNA/Pol II Complexes as a Model System. Methods in Molecular Biology. 165-178. 2015
- A new twist on cell growth control. Cell Cycle. 3474-3475. 2014
- Selection and Characterization of a DNA Aptamer That Can Discriminate between cJun/cJun and cJun/cFos. PLoS One. 2014
- Single molecule studies of RNA polymerase II transcription in vitro. Transcription. 2014
- Single molecule studies of RNA polymerase II transcription in vitro.. Transcription. e27608. 2014
- NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription. Molecular Immunology. 48-56. 2013
- Structural Insights into Transcriptional Repression by Noncoding RNAs That Bind to Human Pol II. Journal of Molecular Biology. 3639-3648. 2013
- The Non-Coding B2 RNA Binds to the DNA Cleft and Active-Site Region of RNA Polymerase II. Journal of Molecular Biology. 3625-3638. 2013
- RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. The EMBO Journal. 781-790. 2013
- The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts. Epigenomics. 95-102. 2013
- Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system.. Methods in Molecular Biology. 203-215. 2013
- Single-Molecule Fluorescence Resonance Energy Transfer Shows Uniformity in TATA Binding Protein-Induced DNA Bending and Heterogeneity in Bending Kinetics. Biochemistry. 7444-7455. 2012
- ERK1/2 activation is a therapeutic target in age-related macular degeneration. Proceedings of the National Academy of Sciences of USA. 13781-13786. 2012
- DICER1 Loss and Alu RNA Induce Age-Related Macular Degeneration via the NLRP3 Inflammasome and MyD88. Cell. 847-859. 2012
- Non-coding RNAs: key regulators of mammalian transcription. Trends in Biochemical Sciences. 144-151. 2012
- DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature. 325-+. 2011
- XPB, a subunit of TFIIH, is a target of the natural product triptolide. Nature Chemical Biology. 182-188. 2011
- B2 RNA represses TFIIH phosphorylation of RNA polymerase II. Transcription. 45-49. 2011
- The C-terminal region of human NFATc2 binds dun to synergistically activate interleukin-2 transcription. Molecular Immunology. 2314-2322. 2010
- Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nature Reviews Genetics. 549-558. 2010
- Dampening DNA binding A common mechanism of transcriptional repression for both ncRNAs and protein domains. RNA Biology. 305-309. 2010
- Genomic gems: SINE RNAs regulate mRNA production. Current Opinion in Genetics and Development. 149-155. 2010
- RNA Polymerase II and TAFs Undergo a Slow Isomerization after the Polymerase Is Recruited to Promoter-Bound TFIID. Journal of Molecular Biology. 57-68. 2010
- Genome-wide insights into eukaryotic transcriptional control.. Genome Biology. 305. 2010
- TFIIF Facilitates Dissociation of RNA Polymerase II from Noncoding RNAs That Lack a Repression Domain. Molecular and Cellular Biology. 91-97. 2010
- InvAluable Junk: The Cellular Impact and Function of Alu and B2 RNAs. IUBMB Life. 831-837. 2009
- In new company: U1 snRNA associates with TAF15. EMBO Reports. 454-456. 2009
- 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 USA. 5569-5574. 2009
- TATA-binding Protein and Transcription Factor IIB Induce Transcript Slipping during Early Transcription by RNA Polymerase II. Journal of Biological Chemistry. 9093-9098. 2009
- From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription. Critical Reviews in Biochemistry and Molecular Biology. 3-15. 2009
- Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Molecular Cell. 499-509. 2008
- TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability. Journal of Molecular Biology. 619-632. 2007
- Characterization of the sequence and architectural constraints of the regulatory and core regions of the human interleukin-2 promoter. Molecular Immunology. 2813-2819. 2007
- Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA. 583-596. 2007
- An RNA transcriptional regulator templates its own regulatory RNA. Nature Chemical Biology. 89-90. 2007
- Nuclear myosin I is necessary for the formation of the first phosphodiester bond during transcription initiation by RNA polymerase II. Journal of Cellular Biochemistry. 1001-1009. 2006
- Non-coding-RNA regulators of RNA polymerase II transcription. Nature Reviews Molecular Cell Biology. 612-616. 2006
- An 8 nt RNA triggers a rate-limiting shift of RNA polymerase II complexes into elongation. The EMBO Journal. 3100-3109. 2006
- Beating the heat: A translation factor and an RNA mobilize the heat shock transcription factor HSF1. Molecular Cell. 153-154. 2006
- Protein-protein interaction assays: eliminating false positive interactions. Nature Methods. 135-139. 2006
- 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. 39860-39869. 2005
- Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II. Nature Cell Biology. 1094-U18. 2004
- B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature Structural and Molecular Biology. 822-829. 2004
- The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature Structural and Molecular Biology. 816-821. 2004
- 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_II250). Journal of Biological Chemistry. 26257-26265. 2004
- In vitro studies of the early steps of RNA synthesis by human RNA polymerase II. Methods in Enzymology. 687-701. 2003
- Binding of beta-actin to TATA binding protein (TBP), pre-initiation complex (PIC) formation and transcription by RNA polymerase II (RNAPII). Molecular Biology of the Cell. 421A-421A. 2002
- Myosin I and transcription by RNA polymerase I and II. Molecular Biology of the Cell. 179A-179A. 2002
- Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions. Journal of Biological Chemistry. 19618-19626. 2002
- Promoter scanning for transcription inhibition with DNA-binding polyamides. Molecular and Cellular Biology. 1723-1733. 2002
- Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape. Molecular and Cellular Biology. 762-773. 2002
- Kinetic and mechanistic analysis of the RNA polymerase II transcription reaction at the human interleukin-2 promoter. Journal of Molecular Biology. 993-1006. 2001
- Kinetic and mechanistic analysis of the RNA polymerase II transcrption reaction at the human interleukin-2 promoter.. Journal of Molecular Biology. 993-1006. 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 Research. art. no.-e98. 2001
- c-Jun binds the N terminus of human TAF(II)250 to derepress RNA polymerase II transcription in vitro. Journal of Biological Chemistry. 25582-25588. 2001
- Human TAF_II130 is a coactivator for NFATp. Molecular and Cellular Biology. 3503-3513. 2001
- A kinetic model for the early steps of RNA synthesis by human RNA polymerase II. Journal of Biological Chemistry. 40483-40491. 2000
- Acetyl coenzyme A stimulates RNA polymerase II transcription and promoter binding by transcription factor IID in the absence of histones. Molecular and Cellular Biology. 1923-1930. 2000
- Characterization of DNA binding, transcriptional activation, and regulated nuclear association of recombinant human NFATp.. BMC Immunology. 1. 2000
- 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 USA. 9232-9237. 1998
- Repression of p53-mediated transcription by MDM2: a dual mechanism. Genes and Development. 1974-1986. 1997
- Contacts in context: promoter specificity and macromolecular interactions in transcription.. Cell. 825-830. 1996
- Molecular cloning and expression of the 32-kDa subunit of human TFIID reveals interactions with VP16 and TFIIB that mediate transcriptional activation.. Proceedings of the National Academy of Sciences of USA. 5788-5792. 1995
- TBP-TAF complexes: selectivity factors for eukaryotic transcription.. Current Opinion in Cell Biology. 403-409. 1994
- Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.. Cell. 145-156. 1994
- Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance.. Genes and Development. 515-524. 1994
- Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB.. Cell. 519-530. 1993
- Drosophila TFIIA-L is processed into two subunits that are associated with the TBP/TAF complex.. Genes and Development. 2235-2245. 1993
- Regulation of open complex formation at the Escherichia coli galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cAMP.. Journal of Molecular Biology. 15-29. 1992
- Competing promoters in prokaryotic transcription.. Trends in Biochemical Sciences. 394-397. 1991
- Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF).. Nucleic Acids Research. 4993-5000. 1990

Teaching

courses taught

BCHM 4761 - Biochemistry Laboratory
Primary Instructor - Fall 2020 / Fall 2021 / Fall 2022 / Fall 2023 / Fall 2024
Two 4-hour periods per week. Introduction to modern biochemical techniques. Topics include enzymology, spectrophotometry, electrophoresis, multi-step protein purification, recombinant DNA techniques and molecular cloning. Formerly CHEM 4761.
BCHM 5801 - Advanced Signal Transduction and Cell Cycle Regulation
Primary Instructor - Spring 2020
Lect. Advanced discussion of current research and literature in signal transduction, including ligands, receptors, and intracellular signaling pathways, as well as control on transcription, chromatin structure, DNA replication, mitosis, and cell cycle progression. Recommended prerequisites: CHEM 5771 and CHEM 5781 and MCDB 5210 or MCDB 5220. Formerly CHEM 5801.
BCHM 6901 - Research in Biochemistry
Primary Instructor - Fall 2019 / Spring 2020 / Fall 2020 / Spring 2021 / Fall 2021 / Fall 2022 / Spring 2023
May be repeated up to 15 total credit hours.
CHEM 4761 - Biochemistry Laboratory
Primary Instructor - Fall 2018
Two 4-hour periods per week. Introduction to modern biochemical techniques. Topics include enzymology, spectrophotometry, electrophoresis, multi-step protein purification, recombinant DNA techniques and molecular cloning. Formerly CHEM 4761.

Background

education and training

Ph.D., Carnegie Mellon University 1991
B.S., University of Scranton 1985

awards and honors

New Inventor of the Year, conferred by Office of Technology Transfer, 2006
Pew Scholar in the Biomedical Sciences, conferred by Pew Charitable Trusts, The, 1999

International Activities

geographic focus

Australia Country
Canada Country
France Country
Israel Country
United Kingdom Country

Other Profiles

ORCID iD

http://orcid.org/0000-0002-5754-8427