Tracy Johnson, Ph.D.

Laboratory Address:
5159 TLSB Terasaki Life Sciences Building

Maria Rowena Ross Chair, Cell Biology and Biochemistry
Professor, Molecular, Cell, and Developmental Biology
Member, Biochemistry, Biophysics & Structural Biology GPB Home Area, Cell & Developmental Biology GPB Home Area, Gene Regulation GPB Home Area, Genetics & Genomics GPB Home Area
Research Interests
Regulation of gene expression is crucial for every function carried out by the cell—from cell growth and proliferation to the cell’s ability to respond to its ever-changing environment. Hence, understanding cellular function and dysfunction is dependent upon deciphering these gene regulatory mechanisms. This is particularly challenging in the case of eukaryotic genes, which are often interrupted by long stretches of noncoding sequences (introns). These are removed from the newly synthesized RNA, and the remaining sequences (exons) are ligated together to form a mature messenger RNA. This process, pre-messenger RNA splicing, is carried out by the spliceosome made up of 5 small nuclear RNAs and over 100 proteins. Correct splicing is crucial to proper gene expression. In fact, it is estimated that over a quarter of all point mutations that lead to genetic disease are caused by defective splicing.

The spliceosome undergoes dynamic rearrangements in order to recognize splicing signals in the RNA and catalyze the splicing reaction. The goal of our research is to decipher the workings of this elegant ribonucleoprotein “machine,” which has become even more intriguing in light of evidence that splicing signals are recognized co-transcriptionally, while the RNA polymerase is still engaged with a chromatin template. Our work is focused on three key areas (i) understanding the molecular details of the spliceosome rearrangements involved in splice site recognition and splicing catalysis; (ii) dissecting how this occurs in the context of transcription, chromatin modification, and other RNA processing events; and (iii) understanding how the cell exploits these mechanisms to respond to its environment.


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.


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.