Dr. John J. Wyrick

Associate Professor, School of Molecular Biosciences, PhD, 2002, M.I.T.
John Wyrick.


Cells respond to environmental or developmental signals by reprogramming the expression of specific genes throughout their genome. We wish to understand the mechanisms by which this occurs. To do so, we have used genomics-based approaches to decipher how gene expression is regulated in the model eukaryote, Saccharomyces cerevisiae, and in the plant, Arabidopsis thaliana. Ongoing projects include the (1) use of DNA microarrays to profile genome-wide mRNA levels in various transcription factor and histone mutant strains; (2) analysis of global protein-DNA interactions using DNA microarrays; (3) the development of various bioinformatics tools to analyze the microarray data, including an online microarray database. These projects involve the development and use of functional genomic tools to investigate how genome expression is regulated in eukaryotic cells.

Selected Publications

Wyrick, J.J.  Computational analysis of promoter elements and chromatin features in yeast.  Methods in Molecular Biology.  2012;809:217-235.

Wyrick, J.J., Kyriss, M.N., Davis, W.B.  Ascending the nucleosome face:  Recognition and function of structured domains in the histone H2A-H2B dimer.  Biochimica et Biophysica Acta – Gene Regulatory Mechanisms.  2012;1819(8):892-901.

Morris, R.T., Doroshenk, K.A., Crofts, A.J., Lewis, N., Okita, T.W., Wyrick, J.J.  RiceRPB:  A database of experimentally identified RNA-binding proteins in Oryza sativa L.  Plant Science.  2011;180(2):204-211.

Doroshenk, K.A., Crofts, A.J., Washida, H., Satoh-Cruz, M., Crofts, N., Sugino, A., Okita, T.W., Morris, R.T., Wyrick, J.J., Fukuda, M., et al.  Characterization of the rice gulp4 mutant suggests a role for the small GTPase Rab5 in the biosynthesis of carbon and nitrogen storage reserves in developing endosperm.  Breeding Science. 2010;60(5):556-567.

Morris, R.T., O’Connor, T.R., Wyrick, J.J.  Ceres:  software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.  Bioinformatics (Oxford, England).  2010;26(2):168-174.

Kyriss, M.N., Jin, Y., Gallegos, I.J., Sanford, J.A., and Wyrick, J.J. (2010) Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage. Mol. Cell. Biol. 30:3503-3518.

Zheng, S., Wyrick, J.J., Reese, J.C. (2010) Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N-terminus of histone H2A. Mol Cell Biol. 30:3635-45.

Nag, R., Kyriss, M., Smerdon, J.W., Wyrick, J.J., Smerdon, M.J. (2010) A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Res. 38:1450-1460.

Jin, Y., Rodriguez, A.M., Wyrick, J.J. (2009) Genetic and Genome-wide Analysis of Simultaneous Mutations in Acetylated and Methylated Lysine Residues in Histone H3 in Saccharomyces cerevisiae. Genetics 181:461-472.

Chaudhuri, S., Wyrick, J.J., Smerdon, M.J. (2009) Histone H3 Lys79 Methylation is Required for Efficient Nucleotide Excision Repair in a Silenced Locus of Saccharomyces cerevisiae. Nucleic Acids Res. 37:1690-1700.