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Ann L Kirchmaier

Biochemistry 

  • Associate Professor of Biochemistry
765.494.0977
765.494.7897
BCHM Room 321

Lab Members

Area of Expertise: Epigenetic processes that mediate heritable modifications to chromatin

The research in my lab focuses on understanding how cells regulate epigenetic processes. Our research examines the role of the cell cycle and DNA replication in assembly or maintenance of chromatin structures and the effects of these structures on DNA replication. We are interested in how the cell restricts heterochromatin to specific genomic loci, why heterochromatin formation is regulated by the cell cycle, how transcription of genes is prevented in silenced regions, and whether epigenetic processes are influenced by or influence events including DNA damage and the initiation of DNA replication. We are intrigued by how epigenetic states are maintained throughout the cell cycle and are duplicated and inherited each time the chromosome itself is replicated and the cell divides. We investigate how environmental factors perturb epigenetic processes and can contribute to inappropriate gene expression, developmental defects, tumorogenesis and other catastrophic disorders.

Our research explores the interface between epigenetic processes, histone modifications, chromatin assembly, DNA replication and the cell cycle, Our laboratory combines molecular biology, biochemical and quantitative microscopy-based approaches with mammalian cell culture and the power of yeast genetics to understand the impact of genetic and external factors on epigenetic gene regulation.

Silencing inSaccharomyces cerevisiae

We use silent chromatin in S. cerevisiae as a model for understanding how epigenetically regulated chromatin structures are established, maintained and inherited. Silenced chromatin in budding yeast, is akin to heterochromatin in organisms such as maize, flies, and mammals. S. cerevisiae uses epigenetically inherited chromosomal structures to regulate a variety of cellular activities including controlling cell-type specific gene expression, modulating ribosomal RNA levels, and preserving telomere structure and stability. Silenced regions in S. cerevisiae that are regulated, in part, by the Silent Information Regulator, or Sir, proteins include the silent mating-type loci, HML and HMR, the rDNA locus and the telomeres.

To mediate silencing at a given site on a chromosome, an organism must first have a way to recruit the proteins that compose silenced chromatin to that locus. In yeast, regulatory sites known as silencers flank the silent mating-type loci. Silencers contain binding sites for the Origin Recognition Complex (ORC), and the transcriptional regulators Rap1p and Abf1p. In addition, the Sir proteins, Sir1p, Sir2p, Sir3p and Sir4p, are structural components of silenced chromatin in yeast. Unlike ORC, Rap1p and Abf1p, however, the Sir proteins do not bind to DNA site-specifically. Instead, Sir proteins associate with silencers through protein-protein interactions between each other, proteins bound at silencers, and histones H3 and H4. Once initiated, silencing spreads along the chromosome over several kilobases of DNA and inactivates gene expression. Once established, the transcriptionally inactive state of this region of the chromosome is maintained throughout the cell cycle and can be stably inherited in subsequent generations. Many proteins involved in silencing in yeast have homologs in a wide variety of organisms, including humans where several are involved in development and differentiation or have been implicated in cancer.

Epigenetic Processes and Replication-Coupled Chromatin Assembly

We are investigating how a network of chromatin assembly factors, histone-modifying enzymes and replication factors interact to assemble appropriately modified nucleosomes during DNA replication and thereby promote epigenetic processes and genome integrity. We have been characterizing how silencing is affected by the DNA polymerase processivity factor PCNA through pathways involving several factors including the chromatin assembly factors Asf1p and CAF-1, the PCNA loading complex RF-C and the histone acetyltransferase Rtt109p. As nucleosomal DNA serves as the foundation upon which silent chromatin is built, perturbations in replication-coupled chromatin assembly can alter the efficiency and location of silent chromatin formation as well as lead to defects in maintaining and inheriting epigenetic states. Repair of DNA damage is also often compromised in mutants with defects linked to histone modifications and replication-coupled chromatin assembly pathways.

Defining the Composition of Chromatin

The simplest structural unit of chromatin, the nucleosome, can exist in a variety of configurations depending on the histone variants and post-translational modifications present. The composition of individual nucleosomes influences chromatin structure and function and provides signals to the cellular machinery to promote gene activation or repression. These signals tend to be dynamic and can vary as a function of the cell cycle or growth conditions. Yet, our understanding of the patterns found within individual nucleosomes and presented to the cellular machinery is limited. Population-based approaches widely used to characterize chromatin composition have been valuable in identifying and mapping individual modifications within histones, but have been limited in describing which modifications are combined within the same nucleosomes. As a powerful complement to standard approaches, we are utilizing single molecule strategies in vitro and in single mammalian and yeast cells to probe epigenetic processes that regulate transcriptional states, responses to DNA damage, centromere function and differentiation in several collaborative projects.

Awards & Honors

(2013) Millionaires Club, College of Agriculture, Purdue University. College of Agriculture, Purdue University.

(2013) University Faculty Scholar. Purdue University.

(2012) Faculty Scholar 2012-2017. Purdue University.

(2012) Seed for Success Award. Purdue University.

(2006) Genetics Society of America Poster Award. The Genetics Society of America.

(2004) Kimmel Scholar Award. The Sidney Kimmel Foundation for Cancer Research.

(2003) Kimmel Scholar Award. The Sidney Kimmel Foundation for Cancer Research.

Selected Publications

Kirchmaier, A. L. (2013). Creating memories of transcription. Proc. Natl. Acad. Sci. USA, 110, 13701-13702. Retrieved from http://www.pnas.org/content/110/34/13701.full.pdf+html

Chen, J., Miller, A., Kirchmaier, A. L., & Irudayaraj, J. M. K. (2012). Single-molecule tools elucidate H2A.Z nucleosome composition.. J. Cell Sci., 125, 2954-2964. Retrieved from http://jcs.biologists.org/content/125/12/2954.full.pdf+html

Young, T. J., & Kirchmaier, A. L. (2012). Cell Cycle Regulation of Silent Chromatin Formation. Biochim. Biophys. Acta, 1819, 303-312. Retrieved from http://ac.els-cdn.com/S1874939911001829/1-s2.0-S1874939911001829-main.pdf?_tid=5b0d693e311053e0f99a75f7f8cdb662&acdnat=1339704549_a37db7c27e84da68aaefbb24174efb0b

Kirchmaier, A. L. (2011). Ub-Family Modifications at the Replication Fork: Regulating PCNA-Interacting Components. FEBS Lett., 585, 2920-2928. Retrieved from http://www.febsletters.org/article/S0014-5793(11)00598-9/

Jacobi, J. L., & Kirchmaier, A. L. (2011). Propagation of Epigenetic States during DNA Replication. In Fundamental Aspects of DNA Replication (Vol. 1st, pp. 245-270). Vienna, Austria: InTech Publishing. Retrieved from http://www.intechopen.com/articles/show/title/propagating-epigenetic-states-during-dna-replication

Miller, A., Chen, J., Takasuka, T. E., Jacobi, J. L., Kaufman, P. D., Irudayaraj, J. M. K., & Kirchmaier, A. L. (2010). Proliferating Cell Nuclear Antigen (PCNA) is Required for Cell Cycle-Regulated Silent Chromatin on Replicated and Nonreplicated Genes. J. Biol. Chem., 285, 35142-35154. Retrieved from http://www.jbc.org/content/early/2010/09/02/jbc.M110.166918.abstract

Yang, B., Miller, A., & Kirchmaier, A. L. (2008). HST3/HST4 - dependent Deacetylation of Lysine 56 of Histone H3 in Silent Chromatin. Mol. Biol. Cell., 19(11), 4993-5005. Retrieved from http://www.molbiolcell.org/cgi/content/full/19/11/4993

Yang, B., Britton, J., & Kirchmaier, A. L. (2008). Insights into the Impact of Histone Acetylation and Methylation on Sir Protein Recruitment, Spreading. J. Mol. Biol., 381(4), 826-844. Retrieved from www.sciencedirect.com/science/article/pii/S0022283608007754

Miller, A., Yang, B., Foster, T., & Kirchmaier, A. L. (2008). Proliferating Cell Nuclear Antigen and ASF1 Modulate Silent Chromatin in Saccharomyces cerevisiae vi. Genetics, 179, 793-809. Retrieved from http://www.genetics.org/cgi/content/full/179/2/793

Yang, B., & Kirchmaier, A. L. (2006). Bypassing the Catalytic Activity of SIR2 for SIR Protein Spreading in S. cerevisiae. Mol. Biol. Cell., 16, 177-192. Retrieved from http://www.molbiolcell.org/cgi/content/full/17/12/5287