Alison McCurdy, Ph.D.

College of Natural & Social Sciences
Department of Chemistry & Biochemistry
Office Location: ASCB 221F
Phone:323-343-2362Email:amccurd@calstatela.edu

Stephen Smale, Ph.D.

Biography:

Stephen T. Smale is a molecular immunologist and biochemist who arrived at UCLA in 1990 as an Assistant Professor in the Department of Microbiology and Immunology within the UCLA School of Medicine. In 1999, he was promoted to Professor and, in 2014, to Distinguished Professor, in the Department of Microbiology, Immunology, and Molecular Genetics, which spans the UCLA College of Letters and Science and the David Geffen School of Medicine. From 1990 to 2007, he was also a Howard Hughes Medical Institute Investigator. Dr. Smale graduated Magna Cum Laude from Cornell University, with Honors and Distinction in Chemistry. He received his Ph.D. in Biochemistry from the University of California, Berkeley under the mentorship of Dr. Robert Tjian. He then was a Helen Hay Whitney Foundation postdoctoral fellow with Nobelist Dr. David Baltimore at the Whitehead Institute, MIT. At UCLA, Dr. Smale previously served as Vice Chair of the Department of Microbiology, Immunology, and Molecular Genetics, Director of Basic and Translational Research for the UCLA Jonsson Comprehensive Cancer Center, Director of the Howard Hughes Medical Institute Science Education Program, Co-Director of the UCLA-Caltech Medical Scientist Training Program, and founding Chair of the School of Medicine’s Research Initiative in Immunity, Inflammation, infection, and Transplantation (I3T). He currently serves as Vice Dean for Research in the David Geffen School of Medicine. The research in Dr. Smale’s laboratory focuses on gene regulation during inflammatory and innate immune responses and during lymphocyte development and leukemogenesis.

Publications

A selected list of publications:

Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST   A stringent systems approach uncovers gene-specific mechanisms regulating inflammation Cell, 2016; 165: 165-179.
Arenzana TL, Schjerven H, Smale ST   Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor Genes & Dev, 2015; 29: 1801-1816.
Lissner ML, Thomas BJ, Wee K, Tong AJ, Kollmann TR, Smale ST   Age-related gene expression differences in monocytes from human neonates, young adults, and older adults, PLoS One, 2015; 10: e0132061.
Smale ST, Tarakhovsky A, Natoli G   Chromatin contributions to the regulation of innate immunity Annual Review of Immunology, 2014; 32: 489-911.
Smale ST   Transcriptional regulation in the immune system: a status report Trends Immunol, 2014; 35: 190-194.
Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON, Smale ST   Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros Nature Immunol, 2013; 14: 1073-1083.
Smale ST, Plevy SE, Weinmann AS, Zhou L, Ramirez-Carrozzi VR, Pope SD, Bhatt DM, Tong AJ   Toward an understanding of the gene-specific and global logic of inducible gene transcription Cold Spring Harb Symp Quant Biol, 2013; 78: 61-68.
Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST   Transcript dynamics of pro inflammatory genes revealed by sequence analysis of subcellular RNA fractions Cell, 2012; 150: 279-290.
Xu J, Smale ST   Designing an enhancer landscape Cell, 2012; 151: 929-931.
Negishi H, Yanai H, Nakajima A, Koshiba R, Atarashi K, Matsuda A, Matsuki K, Miki S, Doi T, Aderem A, Nishio J, Smale ST, Honda K, Taniguchi T   Cross-interference of RLR and TLR signaling pathways modulates antibacterial T cell responses Nature Immunol, 2012; 13: 659-666.
Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML   Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kB family DNA binding Nature Immunol, 2011; 13: 95-102.
Smale ST   Hierarchies of NF-kB target-gene regulation Nature Immunol, 2011; 12: 689-694.
Smale ST   Seq-ing LPS-induced enhancers, Immunity, 2010; 32: 296-297.
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST   A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling Cell, 2009; 138: 114-128.
Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST   Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells Genes & Dev, 2009; 23: 2824-2838.
Carey M, Peterson CL, and Smale ST   Transcriptional regulation in eukaryotes: Concepts, strategies, and techniques, Second edition, , 2009; Cold Spring Harbor Laboratory Press: .
Smale ST, Dorshkind K   Hematopoiesis flies high with Ikaros Nature Immunol, 2006; 7: 367-369.
Li CC, Ramirez-Carrozzi VR, Smale ST   Pursuing global gene regulation “logic” via RNA interference and chromatin immunoprecipitation Nature Immunol, 2006; 7: 692-697.
Ramirez-Carrozzi VR, Nazarian AA, Li CC, Gore SL, Sridharan R, Imbalzano AN, Smale ST   Selective and antagonistic functions of SWI/SNF and Mi-2b nucleosome remodeling complexes during an inflammatory response Genes & Dev, 2006; 20: 282-296.
Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST   A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation Genes & Dev, 2005; 19: 2138-2151.
Su RC, Brown KE, Saaber S, Fisher AG, Merkenschlager M, Smale ST   Dynamic assembly of silent chromatin during thymocyte maturation Nature Genetics, 2004; 36: 502-506.
Papathanasiou P, Perkins AC, Cobb BS, Ferrini R, Sridharan R, Hoyne GF, Nelms KA, Smale ST, Goodnow CC   Widespread failure of hematolymphoid differentiation caused by a recessive niche-filling allele of the Ikaros transcription factor Immunity, 2003; 19: 131-144.
Smale ST, Kadonaga JT   The RNA polymerase II core promoter Annual Review of Biochemistry, 2003; 72: 449-479.
McCarty AS, Kleiger G, Eisenberg D, Smale ST   Selective dimerization of a C2H2 zinc finger subfamily Molecular Cell, 2003; 11: 459-470.
Dovat S, Ronni T, Russell D, Ferrini R, Cobb BS, Smale ST   A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains Genes & Dev, 2002; 16: 2985-2990.
Smale ST and Fisher AG   Chromatin structure and gene regulation in the immune system Annual Review of Immunology, 2002; 20: 427-462.
Smale ST   Core promoters: active contributors to combinatorial gene regulation Genes & Dev, 2001; 15: 2503-2508.
Trinh LA, Ferrini R, Cobb BS, Weinmann AS, Hahm K, Ernst P, Garraway IP, Merkenschlager M, Smale ST   Down-regulation of TDT transcription in CD4(+)CD8(+) thymocytes by Ikaros proteins in direct competition with an Ets activator Genes & Dev, 2001; 15: 1817-1832.
Weinmann AS, Mitchell DM, Sanjabi S, Bradley MN, Hoffmann A, Liou HC, Smale ST   Nucleosome remodeling at the IL-12 p40 promoter is a TLR-dependent, Rel-independent event Nature Immunol, 2001; 2: 51-57.
Cobb BS, Morales-Alcelay S, Kleiger G, Brown KE, Fisher AG, Smale ST   Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding Genes & Dev, 2000; 14: 2146-2160.
Carey M and Smale ST   Transcriptional regulation in eukaryotes: Concepts, strategies, and techniques, , 2000; Cold Spring Harbor Laboratory Press: .
Brightbill HD, Libraty DH, Krutzik SR, Yang RB, Belisle JT, Bleharski JR, Maitland M, Norgard MV, Plevy SE, Smale ST, Brennan PJ, Bloom BR, Godowski PJ, Modlin RL   Host defense mechanisms triggered by microbial lipoproteins through toll-like receptors Science, 1999; 285: 732-736.
Ernst P, Hahm K, Cobb BS, Brown KE, Trinh LA, McCarty AS, Merkenschlager M, Klug CA, Fisher AG, Smale ST   Mechanisms of transcriptional regulation in lymphocyte progenitors: insight from an analysis of the terminal transferase promoter Cold Spr Harb Symp Quant Biol, 1999; 64: 87-97.
Hahm K, Cobb BS, McCarty AS, Brown KE, Klug CA, Lee R, Akashi K, Weissman IL, Fisher AG, and Smale ST   Helios, a T cell-restricted Ikaros family member that quantitatively associates with Ikaros at centromeric heterochromatin Genes & Dev, 1998; 12: 782-796.
Smale ST, Jain A, Kaufmann J, Emami KH, Lo K, Garraway IP   The initiator element: a paradigm for core promoter heterogeneity within metazoan protein-coding genes Cold Spr Harb Symp Quant Biol, 1998; 63: 21-31.
Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG   Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin Cell, 1997; 91: 845-854.
Kaufmann J, Verrijzer CP, Shao J, Smale ST   CIF, an essential cofactor for TFIID-dependent initiator function Genes & Dev, 1996; 10: 873-886.

Tracy Johnson, Ph.D.

Biography

Tracy Johnson is the Maria Rowena Ross Chair of Cell Biology and Biochemistry. Dr. Johnson moved from UC San Diego to UCLA in 2013 to join the faculty in Molecular, Cell, and Developmental Biology. She earned her B.A. in Biochemistry and Cell Biology from UCSD, her Ph.D. in Biochemistry and Molecular Biology from UC Berkeley, and was a Jane Coffin Childs postdoctoral fellow at the California Institute of Technology (Caltech) where she studied the mechanisms of RNA splicing with John Abelson. Dr. Johnson’s research is focused on the mechanisms of eukaryotic RNA processing, particularly pre-messenger RNA splicing. Her lab has most recently been interested in the coordination of these reactions with RNA synthesis and chromatin modification. Dr. Johnson is the recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE) and serves on a number of scientific boards and federal Grant Review panels. In 2013, she received the UCSD Chancellor’s Associates Award for Excellence in Undergraduate Teaching and in 2013 was selected as one of the Top 20 Women Professors in California. In 2014, Dr. Johnson was named a Howard Hughes Medical Institute Professor. As one of 15 leading scientist-educators, the distinction recognizes leadership in research and education, and provides $1 million over five years to create innovative activities that integrate research with undergraduate education.

Publications

A selected list of publications:

Neves Lauren T, Douglass Stephen, Spreafico Roberto, Venkataramanan Srivats, Kress Tracy L, Johnson Tracy L   The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae Genes & development, 2017; 31(7): 702-717.
Venkataramanan Srivats, Douglass Stephen, Galivanche Anoop R, Johnson Tracy L   The chromatin remodeling complex Swi/Snf regulates splicing of meiotic transcripts in Saccharomyces cerevisiae Nucleic acids research, 2017; 45(13): 7708-7721.
Awad Agape M, Venkataramanan Srivats, Nag Anish, Galivanche Anoop Raj, Bradley Michelle C, Neves Lauren T, Douglass Stephen, Clarke Catherine F, Johnson Tracy L   Chromatin-remodeling SWI/SNF complex regulates coenzyme Q6 synthesis and a metabolic shift to respiration in yeast The Journal of biological chemistry, 2017; 292(36): 14851-14866.
Hossain Munshi Azad, Claggett Julia M, Edwards Samantha R, Shi Aishan, Pennebaker Sara L, Cheng Melodyanne Y, Hasty Jeff, Johnson Tracy L   Posttranscriptional Regulation of Gcr1 Expression and Activity Is Crucial for Metabolic Adjustment in Response to Glucose Availability Molecular cell, 2016; 62(3): 346-358.
Johnson Tracy L, Ares Manuel   SMITten by the Speed of Splicing Cell, 2016; 165(2): 265-7.
Davis-Turak Jeremy C, Allison Karmel, Shokhirev Maxim N, Ponomarenko Petr, Tsimring Lev S, Glass Christopher K, Johnson Tracy L, Hoffmann Alexander   Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing Nucleic acids research, 2015; 43(2): 699-707.
Merkhofer Evan C, Hu Peter, Johnson Tracy L   Introduction to cotranscriptional RNA splicing Methods in molecular biology (Clifton, N.J.), 2014; 1126: 83-96.
Hossain Munshi Azad, Johnson Tracy L   Using yeast genetics to study splicing mechanisms Methods in molecular biology (Clifton, N.J.), 2014; 1126: 285-98.
Brangwynne Clifford P, Johnson Tracy L   The micro and macro of RNA function Molecular biology of the cell, 2013; 24(6): 679.
Hossain Munshi Azad, Chung Christina, Pradhan Suman K, Johnson Tracy L   The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription Molecular and cellular biology, 2013; 33(4): 785-99.
Merkhofer Evan C, Johnson Tracy L   U1 snRNA rewrites the “script” Cell, 2012; 150(1): 9-11.
Johnson Tracy L, Vilardell Josep   Regulated pre-mRNA splicing: the ghostwriter of the eukaryotic genome Biochimica et biophysica acta, 2012; 1819(6): 538-45.
Baumgartner Bridget L, Bennett Matthew R, Ferry Michael, Johnson Tracy L, Tsimring Lev S, Hasty Jeff   Antagonistic gene transcripts regulate adaptation to new growth environments Proceedings of the National Academy of Sciences of the United States of America, 2011; 108(52): 21087-92.
Hossain Munshi Azad, Rodriguez Caitlin M, Johnson Tracy L   Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing Nucleic acids research, 2011; 39(19): 8612-27.
McKay Susannah L, Johnson Tracy L   An investigation of a role for U2 snRNP spliceosomal components in regulating transcription PloS one, 2011; 6(1): e16077.
Gunderson Felizza Q, Merkhofer Evan C, Johnson Tracy L   Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements Proceedings of the National Academy of Sciences of the United States of America, 2011; 108(5): 2004-9.