Jeff Ranish, PhD


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, D., Hailu, S., Hada, A., Lee, J., Luo, J., Ranish, J. A., Lin, Y.-C., Feola, K., Persinger, J., Jain, A., Liu, B., Lu, Y., Sen, P., & Bartholomew, B. (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, J., & Ranish, J. (2022). Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes. bioRxiv. Cite Download
Bassett, J., Rimel, J. K., Basu, S., Basnet, P., Luo, J., Engel, K. L., Nagel, M., Woyciehowsky, A., Ebmeier, C. C., Kaplan, C. D., Taatjes, D. J., & Ranish, J. A. (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, E., Zeng, N., Capelle, C. M., Paczia, N., Gillespie, M. A., Kurniawan, H., Benzarti, M., Merz, M. P., Coowar, D., Fritah, S., Vogt Weisenhorn, D. M., Gomez Giro, G., Grusdat, M., Baron, A., Guerin, C., Franchina, D. G., Léonard, C., Domingues, O., Delhalle, S., … Hefeng, F. Q. (2022). PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains Treg homeostasis during ageing. Nature Metabolism, 4(5), 589–607. Cite
Scheer, E., Luo, J., Bernardini, A., Ruffenach, F., Garnier, J.-M., Kolb-Cheynel, I., Gupta, K., Berger, I., Ranish, J., & Tora, L. (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, M., & Ranish, J. A. (2021). Proteomic/transcriptomic analysis of erythropoiesis. Current Opinion in Hematology, 28(3), 150–157. Cite
Jensen, B. C., Phan, I. Q., McDonald, J. R., Sur, A., Gillespie, M. A., Ranish, J. A., Parsons, M., & Myler, P. J. (2021). Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in Leishmania. MSphere, 6(1). Cite
Kim, M. K., Tranvo, A., Hurlburt, A. M., Verma, N., Phan, P., Luo, J., Ranish, J., & Stumph, W. E. (2020). Assembly of SNAPc, Bdp1, and TBP on the U6 snRNA Gene Promoter in Drosophila melanogaster. Molecular and Cellular Biology, 40(12). Cite
Gillespie, M. A., Palii, C. G., Sanchez-Taltavull, D., Perkins, T. J., Brand, M., & Ranish, J. A. (2020). Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry. STAR Protocols, 1(3), 100216. Cite
Wenderski, W., Wang, L., Krokhotin, A., Walsh, J. J., Li, H., Shoji, H., Ghosh, S., George, R. D., Miller, E. L., Elias, L., Gillespie, M. A., Son, E. Y., Staahl, B. T., Baek, S. T., Stanley, V., Moncada, C., Shipony, Z., Linker, S. B., Marchetto, M. C. N., … Gleeson, J. G. (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, M. A., Palii, C. G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W. J. R., Downes, D. J., Sivaraman, K., Espinoza, H. M., Hughes, J. R., Price, N. D., Perkins, T. J., Ranish, J. A., & Brand, M. (2020). Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Molecular Cell, 78(5), 960-974.e11. Cite Download
Mashtalir, N., Suzuki, H., Farrell, D. P., Sankar, A., Luo, J., Filipovski, M., D’Avino, A. R., St Pierre, R., Valencia, A. M., Onikubo, T., Roeder, R. G., Han, Y., He, Y., Ranish, J. A., DiMaio, F., Walz, T., & Kadoch, C. (2020). A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms. Cell, 183(3), 802-817.e24. Cite
Patel, A. B., Moore, C. M., Greber, B. J., Luo, J., Zukin, S. A., Ranish, J., & Nogales, E. (2019). Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. ELife, 8. Cite Download
Hada, A., Hota, S. K., Luo, J., Lin, Y.-C., Kale, S., Shaytan, A. K., Bhardwaj, S. K., Persinger, J., Ranish, J., Panchenko, A. R., & Bartholomew, B. (2019). Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling. Cell Reports, 28(1), 282-294.e6. Cite Download
Luo, J., Bassett, J., & Ranish, J. (2019). Identification of Cross-linked Peptides Using Isotopomeric Cross-linkers. Journal of the American Society for Mass Spectrometry. Cite
Palii, C. G., Cheng, Q., Gillespie, M. A., Shannon, P., Mazurczyk, M., Napolitani, G., Price, N. D., Ranish, J. A., Morrissey, E., Higgs, D. R., & Brand, M. (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, A. B., Louder, R. K., Greber, B. J., Grünberg, S., Luo, J., Fang, J., Liu, Y., Ranish, J., Hahn, S., & Nogales, E. (2018). Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Science (New York, N.Y.), 362(6421). Cite
Kolesnikova, O., Ben-Shem, A., Luo, J., Ranish, J., Schultz, P., & Papai, G. (2018). Molecular structure of promoter-bound yeast TFIID. Nature Communications, 9(1), 4666. Cite Download
Mashtalir, N., D’Avino, A. R., Michel, B. C., Luo, J., Pan, J., Otto, J. E., Zullow, H. J., McKenzie, Z. M., Kubiak, R. L., Pierre, R. S., Valencia, A. M., Poynter, S. J., Cassel, S. H., Ranish, J. A., & Kadoch, C. (2018). Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell, 175(5), 1272-1288.e20. Cite
Tuttle, L. M., Pacheco, D., Warfield, L., Luo, J., Ranish, J., Hahn, S., & Klevit, R. E. (2018). Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Reports, 22(12), 3251–3264. Cite
Pacheco, D., Warfield, L., Brajcich, M., Robbins, H., Luo, J., Ranish, J., & Hahn, S. (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, S., Raman, A. V., Thompson, A. W., Arens, C. E., Gillespie, M. A., von Netzer, F., Hillesland, K. L., Stolyar, S., López García de Lomana, A., Reiss, D. J., Gorman-Lewis, D., Zane, G. M., Ranish, J. A., Wall, J. D., Stahl, D. A., & Baliga, N. S. (2017). Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology, 13(3), 919. Cite
Sen, P., Luo, J., Hada, A., Hailu, S. G., Dechassa, M. L., Persinger, J., Brahma, S., Paul, S., Ranish, J., & Bartholomew, B. (2017). Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex. Cell Reports, 18(9), 2135–2147. Cite
Nakayama, R. T., Pulice, J. L., Valencia, A. M., McBride, M. J., McKenzie, Z. M., Gillespie, M. A., Ku, W. L., Teng, M., Cui, K., Williams, R. T., Cassel, S. H., Qing, H., Widmer, C. J., Demetri, G. D., Irizarry, R. A., Zhao, K., Ranish, J. A., & Kadoch, C. (2017). SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nature Genetics. Cite
McDermott, S. M., Luo, J., Carnes, J., Ranish, J. A., & Stuart, K. (2016). The Architecture of Trypanosoma brucei editosomes. Proceedings of the National Academy of Sciences of the United States of America, 113(42), E6476–E6485. Cite
Warfield, L., Luo, J., Ranish, J., & Hahn, S. (2016). Function of conserved topological regions within the S. cerevisiae basal transcription factor TFIIH. Molecular and Cellular Biology. Cite
Luo, J., Cimermancic, P., Viswanath, S., Ebmeier, C. C., Kim, B., Dehecq, M., Raman, V., Greenberg, C. H., Pellarin, R., Sali, A., Taatjes, D. J., Hahn, S., & Ranish, J. (2015). Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Molecular Cell, 59, 794–806. Cite
Gillespie, M. A., Gold, E. S., Ramsey, S. A., Podolsky, I., Aderem, A., & Ranish, J. A. (2015). An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. The EMBO Journal, 34(9), 1244–1258. Cite
Kapoor, P., Bao, Y., Xiao, J., Luo, J., Shen, J., Persinger, J., Peng, G., Ranish, J., Bartholomew, B., & Shen, X. (2015). Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes & Development, 29(6), 591–602. Cite
Wang, L., Limbo, O., Fei, J., Chen, L., Kim, B., Luo, J., Chong, J., Conaway, R. C., Conaway, J. W., Ranish, J. A., Kadonaga, J. T., Russell, P., & Wang, D. (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), 18566–18571. Cite
Han, Y., Luo, J., Ranish, J., & Hahn, S. (2014). Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex. The EMBO Journal, 33(21), 2534–2546. Cite
Taylor, A. F., Amundsen, S. K., Guttman, M., Lee, K. K., Luo, J., Ranish, J., & Smith, G. R. (2014). Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes. Journal of Molecular Biology, 426(21), 3479–3499. Cite
Knutson, B. A., Luo, J., Ranish, J., & Hahn, S. (2014). Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex. Nature Structural & Molecular Biology, 21(9), 810–816. Cite
Kadoch, C., Hargreaves, D. C., Hodges, C., Elias, L., Ho, L., Ranish, J., & Crabtree, G. R. (2013). Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat Genet. Cite
Sun, B., Utleg, A. G., Hu, Z., Qin, S., Keller, A., Lorang, C., Gray, L., Brightman, A., Lee, D., Alexander, V., Ranish, J., Moritz, R. L., & Hood, L. (2013). Glycocapture-Assisted Global Quantitative Proteomics (gagQP) Reveals Multiorgan Responses in Serum Toxicoproteome. Journal of Proteome Research. Cite
Mirzaei, H., Knijnenburg, T. A., Kim, B., Robinson, M., Picotti, P., Carter, G. W., Li, S., Dilworth, D. J., Eng, J. K., Aitchison, J. D., Shmulevich, I., Galitski, T., Aebersold, R., & Ranish, J. (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), 3645–3650. Cite
Akiyoshi, B., Nelson, C. R., Duggan, N., Ceto, S., Ranish, J., & Biggins, S. (2013). The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet, 9(2), e1003216. Cite
Kloet, S. L., Whiting, J. L., Gafken, P., Ranish, J., & Wang, E. H. (2012). Phosphorylation-Dependent Regulation of Cyclin D1 and Cyclin A Gene Transcription by TFIID Subunits TAF1 and TAF7. Molecular and Cellular Biology, 32(16), 3358–3369. Cite
London, N., Ceto, S., Ranish, J., & Biggins, S. (2012). Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores. Curr Biol, 22, 900–906. Cite
Luo, J., Fishburn, J., Hahn, S., & Ranish, J. (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., Luo, J., Robinson, M., Eng, J., Aebersold, R., & Ranish, J. (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., Isaacs, G. D., Diehl, A. G., Sun, M., Cheung, E., Ranish, J., & Kraus, W. L. (2011). Multiple Sequence-Specific DNA-Binding Proteins Mediate Estrogen Receptor Signaling through a Tethering Pathway. Mol Endocrinol. Cite
Himeda, C. L., Ranish, J., Pearson, R. C., Crossley, M., & Hauschka, S. D. (2010). KLF3 regulates muscle-specific gene expression and synergizes with serum response factor on KLF binding sites. Mol Cell Biol, 30(14), 3430–3443. Cite
Gillespie, M. A., Le Grand, F., Scime, A., Kuang, S., von Maltzahn, J., Seale, V., Cuenda, A., Ranish, J., & Rudnicki, M. A. (2009). p38-gamma-dependent gene silencing restricts entry into the myogenic differentiation program. J Cell Biol, 187(7), 991–1005. Cite
Akiyoshi, B., Nelson, C. R., Ranish, J., & Biggins, S. (2009). Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. Genes Dev, 23(24), 2887–2899. Cite
Akiyoshi, B., Nelson, C. R., Ranish, J., & Biggins, S. (2009). Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae. Genetics, 183(4), 1591–1595. Cite
Chaturvedi, C. P., Hosey, A. M., Palii, C., Perez-Iratxeta, C., Nakatani, Y., Ranish, J., Dilworth, F. J., & Brand, M. (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), 18303–18308. Cite
Liu, Y., Warfield, L., Zhang, C., Luo, J., Allen, J., Lang, W. H., Ranish, J., Shokat, K. M., & Hahn, S. (2009). Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol, 29(17), 4852–4863. Cite
Miles, G. P., Samuel, M. A., Ranish, J., Donohoe, S. M., Sperrazzo, G. M., & Ellis, B. E. (2009). Quantitative proteomics identifies oxidant-induced, AtMPK6-dependent changes in Arabidopsis thaliana protein profiles. Plant Signal Behav, 4(6), 497–505. Cite
Ho, L., Ronan, J. L., Wu, J., Staahl, B. T., Chen, L., Kuo, A., Lessard, J., Nesvizhskii, A. I., Ranish, J., & Crabtree, G. R. (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), 5181–5186. Cite

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

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