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

Liu, Y., J. Ranish, R. Aebersold, and S. Hahn. 2001. “Yeast Nuclear Extract Contains Two Major Forms of RNA Polymerase II Mediator Complexes.” J Biol Chem 276 (10): 7169–75. Cite
Ideker, T., V. Thorsson, J. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. “Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network.” Science 292 (5518): 929–34. Cite
Zhou, H., J. Ranish, J. Watts, and R. Aebersold. 2002. “Quantitative Proteome Analysis by Solid-Phase Isotope Tagging and Mass Spectrometry.” Nat Biotechnol 20 (5): 512–15. Cite
Griffin, T. J., C. M. Lock, X. J. Li, A. Patel, I. Chervetsova, H. Lee, M. E. Wright, J. Ranish, S. S. Chen, and R. Aebersold. 2003. “Abundance Ratio-Dependent Proteomic Analysis by Mass Spectrometry.” Anal Chem 75 (4): 867–74. Cite
Ranish, J., E. C. Yi, D. M. Leslie, S. O. Purvine, D. R. Goodlett, J. Eng, and R. Aebersold. 2003. “The Study of Macromolecular Complexes by Quantitative Proteomics.” Nat Genet 33 (3): 349–55. Cite
Li, X. J., H. Zhang, J. Ranish, and R. Aebersold. 2003. “Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry.” Anal Chem 75 (23): 6648–57. Cite
Ranish, J., S. Hahn, H. Lu, E. C. Yi, X. J. Li, J. Eng, and R. Aebersold. 2004. “Quantitative Proteomics Analysis of an RNA Polymerase II Transcription Complex Identifies TFB5, a New Component of General Transcription Factor IIH.” Mol Cell Biol 24 (4): 1709–20. Cite
Brand, M., J. Ranish, N. T. Kummer, J. Hamilton, K. Igarashi, C. Francastel, T. H. Chi, G. R. Crabtree, R. Aebersold, and M. Groudine. 2004. “Dynamic Changes in Transcription Factor Complexes during Erythroid Differentiation Revealed by Quantitative Proteomics.” Nat Struct Mol Biol 11 (1): 73–80. Cite
Rani, P. G., J. Ranish, and S. Hahn. 2004. “RNA Polymerase II (Pol II)-TFIIF and Pol II-Mediator Complexes: The Major Stable Pol II Complexes and Their Activity in Transcription Initiation and Reinitiation.” Mol Cell Biol 24 (4): 1709–20. Cite
Himeda, C. L., J. Ranish, J. C. Angello, P. Maire, R. Aebersold, and S. D. Hauschka. 2004. “Quantitative Proteomic Identification of Six4 as the Trex-Binding Factor in the Muscle Creatine Kinase Enhancer.” Mol Cell Biol 24 (5): 2132–43. Cite
Warfield, L., J. Ranish, and S. Hahn. 2004. “Positive and Negative Functions of the SAGA Complex Mediated through Interaction of Spt8 with TBP and the N-Terminal Domain of TFIIA.” Genes Dev 18 (9): 1022–34. Cite
Ranish, J., S. Hahn, Y. Lu, E. C. Yi, X. J. Li, J. Eng, and R. Aebersold. 2004. “Identification of TFB5, a New Component of General Transcription and DNA Repair Factor IIH.” Nat Genet 36 (7): 707–13. Cite
Giglia-Mari, G., F. Coin, J. Ranish, D. Hoogstraten, A. Theil, N. Wijgers, N. G. Jaspers, et al. 2004. “A New, Tenth Subunit of TFIIH Is Responsible for the DNA Repair Syndrome Trichothiodystrophy Group A.” Nat Genet 36 (7): 714–19. Cite
Desiere, F., E. W. Deutsch, A. I. Nesvizhskii, P. Mallick, N. L. King, J. K. Eng, A. Aderem, et al. 2005. “Integration with the Human Genome of Peptide Sequences Obtained by High-Throughput Mass Spectrometry.” Genome Biol 6 (1): R9. Cite
King, N. L., E. W. Deutsch, J. Ranish, A. I. Nesvizhskii, J. S. Eddes, P. Mallick, J. Eng, et al. 2006. “Analysis of the Saccharomyces Cerevisiae Proteome with PeptideAtlas.” Genome Biol 7 (11): R106. Cite
Ranish, J., M. Brand, and R. Aebersold. 2007. “Using Stable Isotope Tagging and Mass Spectrometry to Characterize Protein Complexes and to Detect Changes in Their Composition.” Methods Mol Biol 359: 17–35. Cite
Mallick, P., M. Schirle, S. S. Chen, M. R. Flory, H. Lee, D. Martin, J. Ranish, et al. 2007. “Computational Prediction of Proteotypic Peptides for Quantitative Proteomics.” Nat Biotechnol 25 (1): 125–31. Cite
Sun, B., J. Ranish, A. G. Utleg, J. T. White, X. Yan, B. Lin, and L. Hood. 2007. “Shotgun Glycopeptide Capture Approach Coupled with Mass Spectrometry for Comprehensive Glycoproteomics.” Mol Cell Proteomics 6 (1): 141–49. Cite
Heo, K., B. Kim, K. Kim, J. Choi, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Isolation and Characterization of Proteins Associated with Histone H3 Tails in Vivo.” J Biol Chem 282 (21): 15476–83. Cite
Lessard, J., J. I. Wu, J. Ranish, M. Wan, M. M. Winslow, B. T. Staahl, H. Wu, R. Aebersold, I. A. Graef, and G. R. Crabtree. 2007. “An Essential Switch in Subunit Composition of a Chromatin Remodeling Complex during Neural Development.” Neuron 55 (2): 201–15. Cite
Choi, J., B. Kim, K. Heo, K. Kim, H. Kim, Y. Zhan, J. Ranish, and W. An. 2007. “Purification and Characterization of Cellular Proteins Associated with Histone H4 Tails.” J Biol Chem 282 (29): 21024–31. Cite
Demers, C., C. P. Chaturvedi, J. Ranish, G. Juban, P. Lai, F. Morle, R. Aebersold, F. J. Dilworth, M. Groudine, and M. Brand. 2007. “Activator-Mediated Recruitment of the MLL2 Methyltransferase Complex to the Beta-Globin Locus.” Mol Cell 27 (4): 573–84. Cite
Kim, B., A. I. Nesvizhskii, P. G. Rani, S. Hahn, R. Aebersold, and J. Ranish. 2007. “The Transcription Elongation Factor TFIIS Is a Component of RNA Polymerase II Preinitiation Complexes.” Proc Natl Acad Sci U S A 104 (41): 16068–73. Cite
Qi, Y., J. Ranish, X. Zhu, A. Krones, J. Zhang, R. Aebersold, D. W. Rose, M. G. Rosenfeld, and C. Carriere. 2008. “Atbf1 Is Required for the Pit1 Gene Early Activation.” Proc Natl Acad Sci U S A 105 (7): 2481–86. Cite
Rubio, E. D., D. J. Reiss, P. L. Welcsh, C. M. Disteche, G. N. Filippova, N. S. Baliga, R. Aebersold, J. Ranish, and A. Krumm. 2008. “CTCF Physically Links Cohesin to Chromatin.” Proc Natl Acad Sci U S A 105 (24): 8309–14. Cite
Himeda, C. L., J. Ranish, and S. D. Hauschka. 2008. “Quantitative Proteomic Identification of MAZ as a Transcriptional Regulator of Muscle-Specific Genes in Skeletal and Cardiac Myocytes.” Mol Cell Biol 28 (20): 6521–35. Cite
Picotti, P., H. Lam, D. Campbell, E. W. Deutsch, H. Mirzaei, J. Ranish, B. Domon, and R. Aebersold. 2008. “A Database of Mass Spectrometric Assays for the Yeast Proteome.” Nat Methods 5 (11): 913–14. Cite
Kao, S. C., H. Wu, J. Xie, C. P. Chang, J. Ranish, I. A. Graef, and G. R. Crabtree. 2009. “Calcineurin/NFAT Signaling Is Required for Neuregulin-Regulated Schwann Cell Differentiation.” Science 323 (5914): 651–54. 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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

View references that use Nexus.