Research in the Lab of Dr. Amy T. Hark
Welcome to the Hark Lab! We investigate the effects of
DNA packaging and genome organization on gene function.
Please visit us in Room 223, New Science Building.
Statement of Research Interests
Impact of histone acetylation on plant development
Background on HATs
Background on Arabidopsis
Background on Our Research
Comparative genomics in Drosophila
My research interests focus on the regulation of gene transcription in eukaryotic organisms, and the consequences of this regulation for downstream developmental events. In particular, I am interested in how factors such as covalent modifications of histones, chromatin structure/architecture, and gene organization may act and interact to influence gene expression.
Impact of histone acetylation on plant development
One area of current research investigates the biological role of the histone acetyltransferase (HAT) enzyme GCN5 in developmental pathways in the model plant Arabidopsis thaliana. GCN5 can covalently modify histones (chromatin proteins) by catalyzing the addition of acetyl group to specific lysine residues. This modification is hypothesized to affect histone-DNA contacts or provide binding sites for other factors involved in regulating transcription (the histone code hypothesis), but the exact biochemical effects of histone acetylation are still not completely understood. However, there is a well-established correlation between acetylation of histones and activation of gene transcription. Misregulation of histone acetylation states has been implicated in cancer and developmental disorders.
Why study chromatin modifying factors in Arabidopsis?
First, a little bit of background. Arabidopsis is a flowering plant, in the Brassica family, related to plants you are probably more familiar with such as broccoli and cauliflower. Arabidopsis has emerged as an experimental model for a number of reasons, including:
It's easily grown in the laboratory and is a good genetic system, with a relatively short generation time of ~6 weeks and a single individual producing hundreds of seeds.
It's easy to transform, allowing for the production of transgenic plants.
Its genome has been fully sequenced, which along with many other community resources facilitates many aspects of molecular and genetic research.
For me, Arabidopsis also provides a model system to explore gene regulation in the context of its effects on fundamental developmental events, which is one of my areas of interest. Also, there has been a long history of the study of epigenetic effects on gene expression in plants, but very little known about the roles chromatin-modifying factors such as GCN5 might play.
In the lab of Dr. Steven Triezenberg at Michigan State University, my colleague Dr. Kostas Vlachonasios (now at Aristotle University of Thessaloniki, Greece) and I took a reverse genetics approach to understanding the function of transcriptional coactivators in Arabidopsis. We identified mutations in genes encoding the HAT GCN5 and associated factors and studied the resulting phenotype of mutant plants. Plants containing disruptions in either the GCN5 gene or the ADA2b gene displayed dramatic effects with respect to their overall growth (see photos below). These mutants also exibited developmental problems in a variety of plant organs, perhaps most notably defects in their flowers which render the mutants plants infertile. Interestingly, the gcn5 and ada2b mutant plants share some aspects of their phenotype but each mutant also displays unique defects, which suggests that the GCN5 and ADA2b proteins may function together as well as separately to regulate gene expression in plants.
|On the left is a plant that is heterozygous for the gcn5 mutation (gcn5 +/-) that shows a wildtype phenotype. The three plants on the right are homozygous for different disruptions in the GCN5 gene (gcn5 -/-).||
With the overarching goal of understanding GCN5’s role in promoting a developmental program, here at Muhlenberg we undertook a more detailed characterization of the gcn5 mutant phenotype in collaboration with Dr. Elizabeth McCain. We believed this would provide insights in a quest to describe specific GCN5 developmental targets and focused first on flower development. Our research group demonstrated that gcn5-1 and gcn5-5 mutants display overproliferation of young buds and abnormal structures around the inflorescence meristem and also show defects in stamen number and arrangement at later stages. In addition, gcn5-1 mutants specifically have an enlarged undifferentiated shoot apical meristem. This morphological analysis provided temporal and spatial information that along with a rich literature on flower development aided in the identification of GCN5 target genes in the developing flower.
See the following publications for more background information:
Vlachonasios, K.E., M.F. Thomashow, and S.J. Triezenberg. 2003. Disruption Mutations of ADA2b and GCN5 Transcriptional Adaptor Genes Dramatically Affect Arabidopsis Growth, Development, and Gene Expression. Plant Cell 15: 626-638.
Cohen, R.*, J. Schocken*, A. Kaldis, K.E. Vlachonasios, A.T. Hark, and E.R. McCain. 2009. The histone acetyltransferase GCN5 affects the inflorescence meristem and stamen development in Arabidopsis. Planta 230: 1207-1221.
Current Arabidopsis Project
In the course of characterizing gcn5 floral defects, we noted that trichome patterning seems to be altered in gcn5 mutant plants. Given the well-characterized genetics underlying the differentiation of these single-celled structures, we have explored trichome patterning and morphogenesis as a second system in which to characterize molecular targets of GCN5. We have used microscopy to compare trichome structure between gcn5 mutant and wildtype plants in collaboration with Dr. McCain. Our next step involves utilizing this morphological data to identify and test candidate genes that may serve as targets of GCN5 activity.
This project is part of my collaboration with the Genomics Education Partnership (GEP; gep.wustl.edu), a group based at Washington University in St. Louis. In short, this work in comparative genomics involves using in silico (computer-based) analysis to annotate genes in Drosophila species (defining their start/stop sites, exon/intron boundaries, etc.). The underlying biological question is how genome and chromatin organization impacts gene function, which connects to my basic research interests and work of other members of the Hark Lab. This line of experimentation allows students to be part of a large-scale research project and have their work published while increasing their knowledge of fundamental molecular biology and research tools.
See http://www.gep.wustl.edu/ for more information.
There are opportunities for students to carry out research to address these and related questions, working in the fields of genetics, developmental biology, and molecular biology. I encourage you to contact me if you are interested in doing research in the lab, so that we may talk more about your area(s) of interest and potential projects.
Current and Recent Lab Members
Hanna Caiola '18 (above left) and Hannah Molk '18 (above right) started in the lab working on the Drosophila in silico genomics project and then transitioned to wet-lab work investigating putative GCN5 targets that impact trichome development. Sam Tener '18 is spearheading a new colaboration with Dr. Scott Woody and Dr. Rick Amasino at the University of Wisconsin, exploring possible connections between GCN5 and gibberellin signalling in plant development. Emily Chiacchiaro '19 has also joined this latter effort. Both Sam and Emily initially worked on the GEP project.
Patrick Sockler '19 and Josh Shaffer '19 joined the lab in Fall 2017 to work on the comparative genomics project and in Spring 2018 will extend their in silico analysis to mapping transcription start sites. Iffat Imran '20 and Natalie Trachtman '20 are starting work on GEP projects in Spring 2018.
Michael Wagner '17 extended his initial work on a GEP comparative genomics project by researching a Drosophila gene whose human ortholog plays a role in muscular dystrophy. Minnah Sheikh '16 started in the lab as a research assistant in Summer 2014. Minnah continued in the lab by conducting research as independent studies during her junior and senior year.
Tim DeRosa '16 (left) and Max Blumenthal '16 (right) engaged in both our GEP collaborative project and our wet-lab research.
Julia Burns '16 (left, with Dr. Hark) analyzed trichome phenotypes in Summer 2015. Her work was done in collaboration with Dr. Elizabeth McCain and supported by a Vaughan Research Grant.
Michael Lee '14 (not pictured) and Mark Scheuerman '14 (right) worked on gene annotation in Drosophila as part of our collaborative compartive genomics project during the Spring 2013 and Fall 2013 semesters. Mark and Michael also both continued their work into Spring 2014, helping to wrap up a project looking at the function of a plant-specific domain of ADA2b.
Continuing contributions to the GEP project were made by Gabrielle Whitney '15 and Myles Dworkin '15 (both not pictured). Gabrielle continued this work in Fall 2014 and also assessed putative GCN5 targets in trichomes during her senior year.
|Kelly Cann '15 (left) worked on characterizing trichome phenotypes in collaboration with Dr. McCain during the Spring 2013 semester and Academic Year 2013-2014.
|||Edward Quach '14 (left) started in the lab in Fall 2011 as a Research Assistant genotyping the gcn5-6 population. Ed and Cyrus Kuschner '14 (above right) worked on the comparative genomics project in Spring 2012.
Both Ed and Cyrus continued work in the lab during their junior year in the semester in which they were not studying abroad.
Cyrus shifted his focus to uncovering the gene expression differences that underlie the gcn5 trichome phenotype and received a Dean's Grant to support his work in the summer of 2013.
Jenna Kotak '13 (below right) began characterizing the gcn5-6 trichome phenotype in Spring 2011 and continued research in the lab until her graduation. Her Summer 2011 work was funded through the Vaughan Award and she received a Dean's Grant to support her work in the summer of 2012.
Lindsey Shantzer '12 (left) and Anne Bertolet '13 (not pictured) engaged in the GEP project beginning in Fall 2010. Anne continued this work through the Spring 2011 semester while Lindsey transitioned to the ADA2b transgene project. Lindsey returned to the lab in AY 2011-2012, continuing to sort through putative ADA2b transgenic lines and developing PCR assays.
Meredith Colwell '12 (left) worked on several molecular biology projects during Summer 2011 and Fall 2011 and was supported by funds from a Summer Research Collaboration grant.