Research Interests

Regulation of gene expression is crucial for every function carried out by the cell, from cell growth and proliferation to the ability of the cell 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.

Selected Publications

Awad AM, Venkataramanan S, Nag A, Galivanche AR, Bradley MC, Neves LT, Douglass S, Clarke CF, Johnson TL., "Chromatin-remodeling SWI/SNF complex regulates coenzyme Q6 synthesis and a metabolic shift to respiration in yeast", J Biol Chem 292 (36): 14851-14866 (2017).

Venkataramanan, S., Douglass, S., Galivanche, A.R., and T.L. Johnson., "The chromatin remodeling complex Swi/Snf regulates splicing of meiotic transcripts in Saccharomyces cerevisiae", Nucleic Acids Research 45 (13): 7708-7721 (2017). [link]

Neves, L.T., Douglass, S., Spreafico, R., Venkataramanan, S., Kress, T.L. and T.L. Johnson., "The Histone Variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae", Genes & Development 31: 702-717 (2017).

Johnson, T.L. and Ares, M.Jr., "SMITten by the Speed of Splicing", Cell 165 (2): 265-267 (2016).

Merkhofer, E.C., Hu, P., and Johnson, T.L., "Introduction to cotranscriptional RNA splicing", Methods Mol Biol 1126: 83-96 (2014).

Hossain, M.A. and Johnson, T.L., "Using yeast genetics to study RNA splicing", Methods Mol Biol 1126: 285-298 (2014).

Hossain, M.A., Chung, C., Pradhan, S.K., and Johnson, T.L., "The yeast cap binding complex modulates transcription factor recruitment and establishes proper histone H3K36 trimethylation during active transcription", Mol Cell Biol 33 (4): 785-799 (2013).

Brangwynne and Johnson, T.L., "The micro and macro of RNA function", Mol. Biol. Cell 24 (6): (2013).

Merkhofer, E. and Johnson, T.L., "Preview: U1 snRNA writes the script", Cell 150 (1): 9-11 (2012).

Johnson, T.L. and Vilardell, J., "Regulated pre-mRNA splicing: the ghostwriter of the eukaryotic genome", Biochem. Biophys. Acta: Gene Regulatory Mechanisms (2012).

Baumgartner, B.L., Bennett, M.R., Ferry, M., Johnson, T.L., Tsimring, L.S., Hasty, J., "Antagonistic gene transcripts regulate adaptation to new growth environments", Proc Natl Acad Sci USA 108 (52): 21087-21092 (2011).

Hossain, M.A., Rodriguez, C.M., and T.L. Johnson, "Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing", Nucleic Acids Res 39 (19): 8612-8627 (2011).

Gunderson, F.Q., Merkhofer, E.C. and T.L. Johnson, "Dynamic histone acetylation is critical for co-transcriptional spliceosome assembly and spliceosomal rearrangements", Proc Natl Acad Sci USA 108 (5): 2004-2009 (2011).

McKay, S.L. and Johnson, T.L., "An investigation of a role for the U2 snRNP spliceosomal components in regulating transcription", PLoS ONE 6 (1): (2011).

McKay, S. and T.L. Johnson, "A bird?s eye view of post-translational protein modifications and the regulation of spliceosome dynamics", Molecular Biosystems (2010).