R. Keith Slotkin

Transposable elements are stretches of DNA that can duplicate or move from one location in the genome to another. Their ability to replicate has resulted in transposable elements occupying vast amounts of most eukaryotic genomes, including nearly half of the human genome. Although often overlooked or dismissed as “junk DNA”, transposable elements have played an important role in the structure and evolution of the eukaryotic genome.

When transposable elements are active, they cause DNA damage and new mutations by inserting into essential protein-coding genes or by promoting rearrangements and genome instability. To suppress the inherent mutagenic potential of transposable elements, over a billion years ago eukaryotes evolved a genome-wide surveillance system to target transposable elements for inactivation. This process of selective inactivation takes advantage of the transposable element’s propensity to generate double-stranded RNA, which is the trigger for small RNA-based silencing mechanisms. These silencing mechanisms result in either post-transcriptional silencing or chromatin modifications. One such heritable chromatin modification is DNA methylation, which can be propagated from cell to cell (through mitosis) or from parent to progeny (through meiosis and fertilization). This heritable repression of gene expression is referred to as epigenetic regulation, and is not the result of changes in the primary DNA sequence (ATGCs). Epigenetic changes are distinct from genetic changes because they are readily reversible, making them exceptional targets of short-term or generation-to-generation environmental modulation.

For more information on the epigenetic regulation of transposable elements, see Slotkin and Martienssen, 2007, Nature Reviews Genetics.

My laboratory uses Arabidopsis thaliana (thale cress), a reference flowering plant, as a model to investigate basic biological questions exploring how the eukaryotic genome and transposable elements interact over the development of a single generation, as well as across evolutionary time. Plants offer a unique opportunity to study transposable elements. Unlike animals, plants lack a germline that is set-aside early in embryonic development, meaning that epigenetic changes that occur during plant development are more likely to be transmitted to the next generation. Furthermore, plants have evolved a particularly diverse suite of mechanisms for encoding and propagating epigenetic modifications, such as forms of DNA methylation that specifically mark sites targeted by small RNA-based gene silencing. Finally, a wide variety of active transposable elements have been identified and examined in detail in plants.

Studies into the location and timing of transposable element silencing in eukaryotes has led to the identification of germ cells as the key spatial and temporal point of the lifecycle where regulation occurs. Male germ cells (sperm cells) in flowering plants are housed in pollen grains. In Arabidopsis, mature pollen is a three-celled structure, containing two sperm cells embedded into a larger vegetative cell (see picture and movie). Transposable element silencing is lost specifically in the pollen vegetative cell, resulting in the reactivation and mobilization of transposable elements. My laboratory studies transposable element epigenetic regulation at points in the plant life cycle, with particular interest in germ cells and pollen.

For more information on transposable element regulation in pollen, see Slotkin et al, 2009, Cell.

Projects in the laboratory focus on the following:

1. How the cell recognizes which regions of the genome are genes and should be expressed, and which are transposable elements and should be selectively silenced

2. How epigenetic information targeting transposable elements for silencing is propagated from generation to generation, protecting each generation from new mutations

3. How the recruitment of epigenetic control to transposable elements has been co-opted over evolutionary time to produce novel and interesting examples of gene regulation

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3D reconstruction of a mature Arabidopsis pollen grain expressing green GFP in the two sperm cells, and red RFP in the pollen vegetative nucleus. Click movie to play.

Current Lab Members:

• Chris DeFraia (Postdoc)
• Germán Martinez-Arias (Postdoc)
• Andrea McCue (Graduate Student)
• Geethi Nuthikattu (Graduate Student)
• Kaushik Panda (Graduate Student)
• Dalen Fultz (Graduate Student)
• Sarah Reeder (Research Associate)
• Erica Thomas (Undergraduate Research Assistant)
• James Stock (Undergraduate Research Assistant)

Currently Teaching

• MG5601 – Undergraduate level Eukaryotic Molecular Genetics Lab
• MG5700 – Graduate level Systems of Genetic Analysis
• Annual Biology Enhancement Workshop, taught to 7th grade students in conjunction with the Ohio State Young Scholars Program

Publications:

• 2012    G. Martinez-Arias and R. Keith Slotkin. Developmental Reactivation of Transposable Element Silencing in Plants: Functional or Byproduct? Current Opinion in Plant Biology v15 496-502.

• 2012    A.D. McCue and R. Keith Slotkin. Transposable Element Small RNAs as Regulators of Gene Expression. Trends in Genetics v28: 616-623.

• 2012    F. Borges, R. Gardner, T. Lopes, J.P. Calarco, L.C. Boavida, R. Keith Slotkin, R.A Martienssen, and J.D. Becker. FACS-based Purification of Arabidopsis Microspores, Sperm Cells and Vegetative Nuclei. Plant Methods v8: 44.

• 2012    A.D. McCue, S. Nuthikattu, S.H. Reeder and R. Keith Slotkin. Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA. PLoS Genetics v8: e1002474

• 2012    R. Keith Slotkin, Saivageethi Nuthikattu, and Ning Jiang. The Evolutionary Impact of Transposable Elements on Gene and Genome Regulation. In Molecular Biology and Evolution of the Plant Genome. Eds. Johann Greilhuber and Jonathan Wendel. Springer Press, p35-58.

• 2011    Damon Lisch and R. Keith Slotkin. Strategies for Silencing and Escape: The Ancient Struggle Between Transposable Elements and Their Hosts. International Review of Cell and Molecular Biology v292: 119-152.

• 2011    A.D. McCue, M. Cresti, J.A. Feijo and R. Keith Slotkin.  Cytoplasmic connection of sperm cells to the pollen vegetative nucleus: the functional role of the male germ unit revisited. Journal of Experimental Botany v62: 1621-1631.

• 2011    Filipe Borges, Patricia A. Pereira, R. Keith Slotkin, Robert A. Martienssen and Jorg D. Becker. MicroRNA activity in the Arabidopsis male germline. Journal of Experimental Botany v62: 1611-1620.

• 2011    N. Jiang, A.A. Ferguson, R. Keith Slotkin and Damon Lisch. Pack-MULE transposable elements induce directional modification of genes through biased insertion and DNA acquisition.
  Proceedings of the National Academy of Sciences USA v108: 1537-1542.           

• 2010    R. Keith Slotkin. The Epigenetic Control of the Athila family of Retrotransposons in Arabidopsis. Epigenetics v5:483-490.

• 2010    V. Olmedo-Monfil, N. Duran-Figueroa, M. Arteaga-Vazquez, E. Demesa-Arevalo, D. Autran, D. Grimanelli, R.K. Slotkin, R.A. Martienssen, J.-P. Vielle Calzada. Control of Female Gamete Formation by a Non-Cell Autonomous Small RNA Pathway in Arabidopsis. Nature v464:628-632.

• 2009    R. Keith Slotkin, Mathew Vaughn, Milos Tanurdzic, Filipe Borges, Jorg Becker, Jose Feijo and Robert Martienssen. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell v136:461-472.

• 2009    Kousuke Hanada, Veronica Vallejo, Kan Nobuta, R. Keith Slotkin, Damon Lisch, Blake Meyers, Shin-Han Shiu and Ning Jiang. Expression and Functional Indication of Pack-MULEs in Rice. The Plant Cell v21:25-38.

• 2009    R. A. Martienssen, A. Kloc, R. Keith Slotkin and Milos Tanurdzic. Epigenetic Inheritance and Reprogramming in Plants and Fission Yeast. Cold Spring Harbor Symposium on Quantitative Biology, v73:265-271.

• 2008    Milos Tanurdzic, Matthew Vaughn, H. Jiang, T.-J. Lee, R. Keith Slotkin, B. Sosinski, William F. Thompson, Rebecca F. Doerge and Robert A. Martienssen. Epigenomic Consequences of Immortalized Plant Cell Suspension Culture. PLoS Biology v6:e302.

• 2008    Eyal Gruntman*, YiJun Qi*, R. Keith Slotkin*, Ted Roeder, Robert Martienssen and Ravi Sachidanandam. Kismeth: Analyzer of Plant Methylation States Through Bisulfite Sequencing. BMC Bioinformatics v9:e371.  *These authors contributed equally to this manuscript

• 2007    R. Keith Slotkin and Robert A. Martienssen. Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics v8:272-285.

• 2005    R. Keith Slotkin, Michael Freeling and Damon Lisch. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nature Genetics v37:641-644.

• 2003    R. Keith Slotkin, Michael Freeling and Damon Lisch. Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. Genetics v165:781-797.

Grants, Fellowships and Awards

• 2013-2018   
  NSF CAREER Grant, Molecular and Cellular Biosciences, Genetic Mechanisms.
  Title: “The Mechanism and Genome-Wide Regulation of Genes and Transposable Elements by Epigenetically Active Small Interfering RNAs”

• 2013    Kavli Fellow, US National Academy of Sciences

• 2010    Early Career Award from the American Society of Plant Biologists

• NSF Molecular and Cellular Biosciences, Genes and Genome Systems Cluster.
  Title: “Defining the role of nurse cells in the propagation of transposable element epigenetic silencing”