Biochemistry & Biophysics

Mary Bryk

bryk Associate Professor of Biochemistry and Biophysics
Phone: (979) 862-2294
Email: bryk@tamu.edu
B.Sc. Cornell University (1985)
M.S. Albany Medical College (1991)
Ph.D. Albany Medical College (1994)
Postdoc. Wadsworth Center, Albany (1995-1997); Harvard Medical School, Boston (1997-2002)
Joined Texas A&M faculty in 2002

Transcriptional Silencing/Chromatin Structure
How cells regulate gene expression is fundamental to most aspects of biology. Research in our laboratory focuses on understanding how gene expression is regulated in inactive or transcriptionally silenced regions of a genome. Our experiments are performed in the yeast Saccharomyces cerevisiae. We identify proteins that regulate transcriptional silencing using classical and modern genetic techniques. Then we investigate how these factors contribute to transcriptional silencing using a combination of genetic, molecular, and biochemical methods.

Our studies focus on silencing of genes inserted in the ribosomal DNA (rDNA) locus. In our early studies, we found that yeast retrotransposons, known as Ty1 elements, are silenced when they integrate into the rDNA locus. Thus, we use genetically marked Ty1 elements, as well as more traditional marker genes, to identify and characterize proteins that regulate transcriptional silencing in the rDNA.

Research from our lab and others has identified several proteins that regulate transcriptional silencing through effects on chromatin structure. These proteins include histones, rDNA-binding proteins and histone-modifying enzymes. Some of these proteins also influence gene expression at other silenced regions of the yeast genome. The chromatin structure of the rDNA is not only important for maintaining transcriptional silencing but also for repressing genetic recombination. Alterations in the level of recombination at the rDNA can decrease the stability of the locus and may lead to premature aging and death.

The goal of our lab is to learn more about the ways that cells regulate transcriptional silencing. Our findings will increase our understanding of how chromatin dynamics influence gene expression and how cells maintain the integrity of their genome. Many of the factors we study have homologues in human cells indicating that our discoveries may provide insight into mechanisms that regulate gene expression in higher eukaryotes.

Recent Publications
  1. Blank HM, Li C, Mueller JE, Bogomolnaya LM, Bryk M & Polymenis M (2008) An increase in mitochondrial DNA promotes nuclear DNA replication in yeast. PLoS Genet 4: e1000047
  2. Li C, Mueller JE, Elfline M & Bryk M (2008) Linker histone H1 represses recombination at the ribosomal DNA locus in the budding yeast Saccharomyces cerevisiae. Mol Microbiol 67: 906-19
  3. Mueller JE, Li C & Bryk M (2007) Isw2 regulates gene silencing at the ribosomal DNA locus in Saccharomyces cerevisiae. Biochem Biophys Res Commun 361: 1017-21
  4. Mueller JE & Bryk M (2007) Isw1 acts independently of the Isw1a and Isw1b complexes in regulating transcriptional silencing at the ribosomal DNA locus in Saccharomyces cerevisiae. J Mol Biol 371: 1-10
  5. Li C, Mueller JE & Bryk M (2006) Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer. Mol Biol Cell 17: 3848-59
  6. Mueller JE, Canze M & Bryk M (2006) The requirements for COMPASS and Paf1 in transcriptional silencing and methylation of histone H3 in Saccharomyces cerevisiae. Genetics 173: 557-67
  7. Bryk M, Briggs SD, Strahl BD, Curcio MJ, Allis CD & Winston F (2002) Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisiae by a Sir2-independent mechanism. Curr Biol 12: 165-70
  8. Briggs SD, Bryk M, Strahl BD, Cheung WL, Davie JK, Dent SY, Winston F & Allis CD (2001) Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev 15: 3286-95
  9. Bryk M, Banerjee M, Conte D Jr & Curcio MJ (2001) The Sgs1 helicase of Saccharomyces cerevisiae inhibits retrotransposition of Ty1 multimeric arrays. Mol Cell Biol 21: 5374-88
  10. Bryk M, Banerjee M, Murphy M, Knudsen KE, Garfinkel DJ & Curcio MJ (1997) Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev 11: 255-69
  11. Mueller JE, Smith D, Bryk M & Belfort M (1995) Intron-encoded endonuclease I-TevI binds as a monomer to effect sequential cleavage via conformational changes in the td homing site. EMBO J 14: 5724-35
  12. Bryk M, Belisle M, Mueller JE & Belfort M (1995) Selection of a remote cleavage site by I-tevI, the td intron-encoded endonuclease. J Mol Biol 247: 197-210
  13. Bryk M, Quirk SM, Mueller JE, Loizos N, Lawrence C & Belfort M (1993) The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target. EMBO J 12: 4040-1
  14. Bryk M, Quirk SM, Mueller JE, Loizos N, Lawrence C & Belfort M (1993) The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target. EMBO J 12: 2141-9
  15. Bell-Pedersen D, Quirk SM, Bryk M & Belfort M (1991) I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target. Proc Natl Acad Sci U S A 88: 7719-23
  16. Bryk M & Belfort M (1990) Spontaneous shuffling of domains between introns of phage T4. Nature 346: 394-6
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