Jeff Ranish, PhD


Jeff Ranish

Dr. Ranish’s formal training is in biochemistry and molecular biology. He did his undergraduate work in biochemistry at Cornell University, and earned his Ph.D. in molecular and cellular biology from the University of Washington. During his doctoral dissertation, Dr. Ranish studied the molecular mechanism of transcription initiation by RNA polymerase II in the laboratory of Dr. Steven Hahn at the Fred Hutchinson Cancer Research Center. Using the yeast Saccharomyces cerevisiae, he applied biochemical, molecular biology, and molecular genetics approaches to address this problem. Dr. Ranish’s studies culminated in the identification and cloning of the genes encoding the general transcription factor TFIIA, and the development of an immobilized promoter system for isolating and studying transcription complexes. He used this system to define intermediates in the formation of preinitiation complexes, and to define the reinitiation complex. For his postdoctoral training, Dr. Ranish worked with Dr. John Yates, III and Dr. Ruedi Aebersold in the Molecular Biotechnology department at the University of Washington where he developed his skills in mass spectrometry based-proteomic technologies. Dr. Ranish joined Dr. Aebersold when he left the University of Washington to found the ISB in 2000.

During his tenure in Dr. Aebersold’s lab, Dr. Ranish developed a new strategy for studying macromolecular complexes by quantitative mass spectrometry. The strategy can be used to determine the composition of complexes and to detect changes in complex composition. It is based on the use of stable isotope tagging of proteins and mass spectrometry to compare the relative abundances of tryptic peptides derived from suitable pairs of purified or partially purified protein complexes. Application of the technology to study transcription factor complexes from yeast and higher eukaryotes has resulted in the discovery of new transcription factors with roles in human health, and has revealed mechanisms for how genes are regulated during development. The usefulness of the approach is apparent from the extensive local, national, and international collaborations that Dr. Ranish engages in.

PhD, Molecular and Cellular Biology Program University of Washington, 1999

Proteomics, macromolecular complexes and transcriptional regulation

Saha, Dhurjhoti, Solomon Hailu, Arjan Hada, Junwoo Lee, Jie Luo, Jeff A. Ranish, Yuan-Chi Lin, et al. 2023. “The AT-Hook Is an Evolutionarily Conserved Auto-Regulatory Domain of SWI/SNF Required for Cell Lineage Priming.” Nature Communications 14 (1): 4682. Cite Download
Luo, Jie, and Jeff Ranish. 2022. “Isobaric Crosslinking Mass Spectrometry Technology for Studying Conformational and Structural Changes in Proteins and Complexes.” bioRxiv. Cite Download
Bassett, Jacob, Jenna K. Rimel, Shrabani Basu, Pratik Basnet, Jie Luo, Krysta L. Engel, Michael Nagel, et al. 2022. “Systematic Mutagenesis of TFIIH Subunit P52/Tfb2 Identifies Residues Required for XPB/Ssl2 Subunit Function and Genetic Interactions with TFB6.” The Journal of Biological Chemistry 298 (10): 102433. Cite Download
Danileviciute, Egle, Ni Zeng, Christophe M. Capelle, Nicole Paczia, Mark A. Gillespie, Henry Kurniawan, Mohaned Benzarti, et al. 2022. “PARK7/DJ-1 Promotes Pyruvate Dehydrogenase Activity and Maintains Treg Homeostasis during Ageing.” Nature Metabolism 4 (5): 589–607. Cite
Scheer, Elisabeth, Jie Luo, Andrea Bernardini, Frank Ruffenach, Jean-Marie Garnier, Isabelle Kolb-Cheynel, Kapil Gupta, Imre Berger, Jeff Ranish, and László Tora. 2021. “TAF8 Regions Important for TFIID Lobe B Assembly or for TAF2 Interactions Are Required for Embryonic Stem Cell Survival.” The Journal of Biological Chemistry, 101288. Cite
Brand, Marjorie, and Jeffrey A. Ranish. 2021. “Proteomic/Transcriptomic Analysis of Erythropoiesis.” Current Opinion in Hematology 28 (3): 150–57. Cite
Jensen, Bryan C., Isabelle Q. Phan, Jacquelyn R. McDonald, Aakash Sur, Mark A. Gillespie, Jeffrey A. Ranish, Marilyn Parsons, and Peter J. Myler. 2021. “Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in Leishmania.” MSphere 6 (1). Cite
Gillespie, Mark A., Carmen G. Palii, Daniel Sanchez-Taltavull, Theodore J. Perkins, Marjorie Brand, and Jeffrey A. Ranish. 2020. “Absolute Quantification of Transcription Factors in Human Erythropoiesis Using Selected Reaction Monitoring Mass Spectrometry.” STAR Protocols 1 (3): 100216. Cite
Wenderski, Wendy, Lu Wang, Andrey Krokhotin, Jessica J. Walsh, Hongjie Li, Hirotaka Shoji, Shereen Ghosh, et al. 2020. “Loss of the Neural-Specific BAF Subunit ACTL6B Relieves Repression of Early Response Genes and Causes Recessive Autism.” Proceedings of the National Academy of Sciences of the United States of America. Cite Download
Gillespie, Mark A., Carmen G. Palii, Daniel Sanchez-Taltavull, Paul Shannon, William J. R. Longabaugh, Damien J. Downes, Karthi Sivaraman, et al. 2020. “Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis.” Molecular Cell 78 (5): 960-974.e11. Cite Download
Mashtalir, Nazar, Hiroshi Suzuki, Daniel P. Farrell, Akshay Sankar, Jie Luo, Martin Filipovski, Andrew R. D’Avino, et al. 2020. “A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms.” Cell 183 (3): 802-817.e24. Cite
Kim, Mun Kyoung, An Tranvo, Ann Marie Hurlburt, Neha Verma, Phuc Phan, Jie Luo, Jeff Ranish, and William E. Stumph. 2020. “Assembly of SNAPc, Bdp1, and TBP on the U6 SnRNA Gene Promoter in Drosophila Melanogaster.” Molecular and Cellular Biology. Cite
Patel, Avinash B., Camille M. Moore, Basil J. Greber, Jie Luo, Stefan A. Zukin, Jeff Ranish, and Eva Nogales. 2019. “Architecture of the Chromatin Remodeler RSC and Insights into Its Nucleosome Engagement.” ELife 8. Cite Download
Hada, Arjan, Swetansu K. Hota, Jie Luo, Yuan-Chi Lin, Seyit Kale, Alexey K. Shaytan, Saurabh K. Bhardwaj, et al. 2019. “Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling.” Cell Reports 28 (1): 282-294.e6. Cite Download
Luo, Jie, Jacob Bassett, and Jeff Ranish. 2019. “Identification of Cross-Linked Peptides Using Isotopomeric Cross-Linkers.” Journal of the American Society for Mass Spectrometry. Cite
Palii, Carmen G., Qian Cheng, Mark A. Gillespie, Paul Shannon, Michalina Mazurczyk, Giorgio Napolitani, Nathan D. Price, et al. 2019. “Single-Cell Proteomics Reveal That Quantitative Changes in Co-Expressed Lineage-Specific Transcription Factors Determine Cell Fate.” Cell Stem Cell 24 (5): 812-820.e5. Cite
Patel, Avinash B., Robert K. Louder, Basil J. Greber, Sebastian Grünberg, Jie Luo, Jie Fang, Yutong Liu, Jeff Ranish, Steve Hahn, and Eva Nogales. 2018. “Structure of Human TFIID and Mechanism of TBP Loading onto Promoter DNA.” Science (New York, N.Y.) 362 (6421). Cite
Kolesnikova, Olga, Adam Ben-Shem, Jie Luo, Jeff Ranish, Patrick Schultz, and Gabor Papai. 2018. “Molecular Structure of Promoter-Bound Yeast TFIID.” Nature Communications 9 (1): 4666. Cite Download
Mashtalir, Nazar, Andrew R. D’Avino, Brittany C. Michel, Jie Luo, Joshua Pan, Jordan E. Otto, Hayley J. Zullow, et al. 2018. “Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes.” Cell 175 (5): 1272-1288.e20. Cite
Tuttle, Lisa M., Derek Pacheco, Linda Warfield, Jie Luo, Jeff Ranish, Steven Hahn, and Rachel E. Klevit. 2018. “Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.” Cell Reports 22 (12): 3251–64. Cite
Pacheco, Derek, Linda Warfield, Michelle Brajcich, Hannah Robbins, Jie Luo, Jeff Ranish, and Steven Hahn. 2018. “Transcription Activation Domains of the Yeast Factors Met4 and Ino2: Tandem Activation Domains with Properties Similar to the Yeast Gcn4 Activator.” Molecular and Cellular Biology. Cite
Turkarslan, Serdar, Arjun V. Raman, Anne W. Thompson, Christina E. Arens, Mark A. Gillespie, Frederick von Netzer, Kristina L. Hillesland, et al. 2017. “Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment.” Molecular Systems Biology 13 (3): 919. Cite
Sen, Payel, Jie Luo, Arjan Hada, Solomon G. Hailu, Mekonnen Lemma Dechassa, Jim Persinger, Sandipan Brahma, Somnath Paul, Jeff Ranish, and Blaine Bartholomew. 2017. “Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex.” Cell Reports 18 (9): 2135–47. Cite
Nakayama, Robert T., John L. Pulice, Alfredo M. Valencia, Matthew J. McBride, Zachary M. McKenzie, Mark A. Gillespie, Wai Lim Ku, et al. 2017. “SMARCB1 Is Required for Widespread BAF Complex-Mediated Activation of Enhancers and Bivalent Promoters.” Nature Genetics. Cite
McDermott, Suzanne M., Jie Luo, Jason Carnes, Jeff A. Ranish, and Kenneth Stuart. 2016. “The Architecture of Trypanosoma Brucei Editosomes.” Proceedings of the National Academy of Sciences of the United States of America 113 (42): E6476–85. Cite
Warfield, Linda, Jie Luo, Jeffrey Ranish, and Steven Hahn. 2016. “Function of Conserved Topological Regions within the S. Cerevisiae Basal Transcription Factor TFIIH.” Molecular and Cellular Biology. Cite
Luo, J., P. Cimermancic, S. Viswanath, C. C. Ebmeier, B. Kim, M. Dehecq, V. Raman, et al. 2015. “Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH.” Molecular Cell 59 (September): 794–806. Cite
Gillespie, Mark A., Elizabeth S. Gold, Stephen A. Ramsey, Irina Podolsky, Alan Aderem, and Jeffrey A. Ranish. 2015. “An LXR-NCOA5 Gene Regulatory Complex Directs Inflammatory Crosstalk-Dependent Repression of Macrophage Cholesterol Efflux.” The EMBO Journal 34 (9): 1244–58. Cite
Kapoor, Prabodh, Yunhe Bao, Jing Xiao, Jie Luo, Jianfeng Shen, Jim Persinger, Guang Peng, Jeff Ranish, Blaine Bartholomew, and Xuetong Shen. 2015. “Regulation of Mec1 Kinase Activity by the SWI/SNF Chromatin Remodeling Complex.” Genes & Development 29 (6): 591–602. Cite
Wang, Lanfeng, Oliver Limbo, Jia Fei, Lu Chen, Bong Kim, Jie Luo, Jenny Chong, et al. 2014. “Regulation of the Rhp26ERCC6/CSB Chromatin Remodeler by a Novel Conserved Leucine Latch Motif.” Proceedings of the National Academy of Sciences of the United States of America 111 (52): 18566–71. Cite
Han, Yan, Jie Luo, Jeffrey Ranish, and Steven Hahn. 2014. “Architecture of the Saccharomyces Cerevisiae SAGA Transcription Coactivator Complex.” The EMBO Journal 33 (21): 2534–46. Cite
Taylor, Andrew F., Susan K. Amundsen, Miklos Guttman, Kelly K. Lee, Jie Luo, Jeffrey Ranish, and Gerald R. Smith. 2014. “Control of RecBCD Enzyme Activity by DNA Binding- and Chi Hotspot-Dependent Conformational Changes.” Journal of Molecular Biology 426 (21): 3479–99. Cite
Knutson, Bruce A., Jie Luo, Jeffrey Ranish, and Steven Hahn. 2014. “Architecture of the Saccharomyces Cerevisiae RNA Polymerase I Core Factor Complex.” Nature Structural & Molecular Biology 21 (9): 810–16. Cite
Kadoch, C., D. C. Hargreaves, C. Hodges, L. Elias, L. Ho, J. Ranish, and G. R. Crabtree. 2013. “Proteomic and Bioinformatic Analysis of Mammalian SWI/SNF Complexes Identifies Extensive Roles in Human Malignancy.” Nat Genet, May. Cite
Sun, B., A. G. Utleg, Z. Hu, S. Qin, A. Keller, C. Lorang, L. Gray, et al. 2013. “Glycocapture-Assisted Global Quantitative Proteomics (GagQP) Reveals Multiorgan Responses in Serum Toxicoproteome.” Journal of Proteome Research, March. Cite
Mirzaei, H., T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, et al. 2013. “Systematic Measurement of Transcription Factor-DNA Interactions by Targeted Mass Spectrometry Identifies Candidate Gene Regulatory Proteins.” Proceedings of the National Academy of Sciences of the United States of America 110 (9): 3645–50. Cite
Akiyoshi, B., C. R. Nelson, N. Duggan, S. Ceto, J. Ranish, and S. Biggins. 2013. “The Mub1/Ubr2 Ubiquitin Ligase Complex Regulates the Conserved Dsn1 Kinetochore Protein.” PLoS Genet 9 (2): e1003216. Cite
Kloet, S. L., J. L. Whiting, P. Gafken, J. Ranish, and E. H. Wang. 2012. “Phosphorylation-Dependent Regulation of Cyclin D1 and Cyclin A Gene Transcription by TFIID Subunits TAF1 and TAF7.” Molecular and Cellular Biology 32 (16): 3358–69. Cite
London, Nitobe, Steven Ceto, J. Ranish, and Sue Biggins. 2012. “Phosphoregulation of Spc105 by Mps1 and PP1 Regulates Bub1 Localization to Kinetochores.” Curr Biol 22 (May): 900–906. Cite
Luo, J., J. Fishburn, S. Hahn, and J. Ranish. 2012. “An Integrated Chemical Cross-Linking and Mass Spectrometry Approach to Study Protein Complex Architecture and Function.” Molecular & Cellular Proteomics : MCP 11 (2): M111 008318. Cite
Yan, W., J. Luo, M. Robinson, J. Eng, R. Aebersold, and J. Ranish. 2011. “Index-Ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures.” Mol Cell Proteomics 10 (3): M110 005611. Cite
Heldring, N., G. D. Isaacs, A. G. Diehl, M. Sun, E. Cheung, J. Ranish, and W. L. Kraus. 2011. “Multiple Sequence-Specific DNA-Binding Proteins Mediate Estrogen Receptor Signaling through a Tethering Pathway.” Mol Endocrinol, February. Cite
Himeda, C. L., J. Ranish, R. C. Pearson, M. Crossley, and S. D. Hauschka. 2010. “KLF3 Regulates Muscle-Specific Gene Expression and Synergizes with Serum Response Factor on KLF Binding Sites.” Mol Cell Biol 30 (14): 3430–43. Cite
Gillespie, M. A., F. Le Grand, A. Scime, S. Kuang, J. von Maltzahn, V. Seale, A. Cuenda, J. Ranish, and M. A. Rudnicki. 2009. “P38-Gamma-Dependent Gene Silencing Restricts Entry into the Myogenic Differentiation Program.” J Cell Biol 187 (7): 991–1005. Cite
Akiyoshi, B., C. R. Nelson, J. Ranish, and S. Biggins. 2009. “Quantitative Proteomic Analysis of Purified Yeast Kinetochores Identifies a PP1 Regulatory Subunit.” Genes Dev 23 (24): 2887–99. Cite
Akiyoshi, B., C. R. Nelson, J. Ranish, and S. Biggins. 2009. “Analysis of Ipl1-Mediated Phosphorylation of the Ndc80 Kinetochore Protein in Saccharomyces Cerevisiae.” Genetics 183 (4): 1591–95. Cite
Chaturvedi, C. P., A. M. Hosey, C. Palii, C. Perez-Iratxeta, Y. Nakatani, J. Ranish, F. J. Dilworth, and M. Brand. 2009. “Dual Role for the Methyltransferase G9a in the Maintenance of Beta-Globin Gene Transcription in Adult Erythroid Cells.” Proc Natl Acad Sci U S A 106 (43): 18303–8. Cite
Liu, Y., L. Warfield, C. Zhang, J. Luo, J. Allen, W. H. Lang, J. Ranish, K. M. Shokat, and S. Hahn. 2009. “Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex.” Mol Cell Biol 29 (17): 4852–63. Cite
Miles, G. P., M. A. Samuel, J. Ranish, S. M. Donohoe, G. M. Sperrazzo, and B. E. Ellis. 2009. “Quantitative Proteomics Identifies Oxidant-Induced, AtMPK6-Dependent Changes in Arabidopsis Thaliana Protein Profiles.” Plant Signal Behav 4 (6): 497–505. Cite
Ho, L., J. L. Ronan, J. Wu, B. T. Staahl, L. Chen, A. Kuo, J. Lessard, A. I. Nesvizhskii, J. Ranish, and G. R. Crabtree. 2009. “An Embryonic Stem Cell Chromatin Remodeling Complex, EsBAF, Is Essential for Embryonic Stem Cell Self-Renewal and Pluripotency.” Proc Natl Acad Sci U S A 106 (13): 5181–86. Cite

The Nexus program is a database search program for crosslinking peptides for MS2 spectra on high accurate mass spectrometry.

View references that use Nexus.