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R. Keith Slotkin

Associate Professor of Biological Sciences
Principal Investigator, Donald Danforth Plant Science Center
PhD, 2005 University of California, Berkeley

Office: Donald Danforth Plant Science Center
Phone: 3145871201
Additional: Website, Twitter, Google-Scholar
Headshot of R. Keith Slotkin


Research summary

Determining how transposable elements become epigenetically silenced

Research description

Transposable elements are fragments of DNA that can duplicate or move from one location 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 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.

My laboratory uses Arabidopsis thaliana (thale cress), a reference flowering plant, as a model to investigate basic biological questions exploring how eukaryotic cells repress transposable elements 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, mutations in the genes responsible for epigenetically suppressing transposable elements in plants are viable, while the corresponding mutations that act similarly to silence transposable elements in mammals are embryonic lethal.

Projects in the laboratory focus on the following:

    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

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

    Determining how active transposable elements are initially triggered for silencing and how epigenetic modifications are first targeted.

    Understanding 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.

To view my plea to the biology community not to overlook transposable elements, see:
Slotkin, R. K. (2018) The case for not masking away repetitive DNA. Mobile DNA, 9(1), p. 475.

For more information on the epigenetic regulation of transposable elements, see:
Sigman, M. J. and Slotkin, R. K. (2016) The first rule of plant transposable element silencing: location, location, location. The Plant Cell, 28(2), pp. 304–313.

For more information on the mechanisms of small RNA-directed DNA Methylation, see:
Cuerda-Gil, D. and Slotkin, R. K. (2016) Non-canonical RNA-directed DNA methylation. Nature Plants, 2(11), p. 16163.

Select Publications

Select Publications

Doherty, C., Friesner, J., Gregory, B., Loraine, A., Megraw, M., Provart, N., Slotkin, R.K., Town, C., Assmann, S.M., Axtell, M., Berardini, T., Chen, S., Gehan, M., Huala, E., Jaiswal, P., Larson, S., Li, S., May, S., Michael, T., Pires, C., Topp, C., Walley, J., Wurtele, E., International Arabidopsis Informatics Consortium Arabidopsis ioinformatics resources: The current state, challenges, and priorities for the future (2019) Plant Direct, 3 (1), art. no. e00109, . DOI: 10.1002/pld3.109

Zhang, Y., Ramming, A., Heinke, L., Altschmied, L., Slotkin, R.K., Becker, J.D., Kappel, C., Lenhard, M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development (2019) Plant Journal, DOI: 10.1111/tpj.14348

Jupe, F., Rivkin, A.C., Michael, T.P., Zander, M., Motley, S.T., Sandoval, J.P., Keith Slotkin, R., Chen, H., Castanon, R., Nery, J.R., Ecker, J.R. The complex architecture and epigenomic impact of plant T-DNA insertions (2019) PLoS Genetics, 15 (1), art. no. e1007819, . DOI: 10.1371/journal.pgen.1007819

Choudury, S.G., Shahid, S., Cuerda-Gil, D., Pand, K., Cullen, A., Ashraf, Q., Sigman, M.J., McCue, A.D., Slotkin, R.K. The RNA export factor ALY1 enables genome-wide rna-directed dna methylation (2019) Plant Cell, 31 (4), pp. 759-774. DOI: 10.1105/tpc.18.00624

Martinez, G., Wolff, P., Wang, Z., Moreno-Romero, J., Santos-González, J., Conze, L.L., Defraia, C., Slotkin, R.K., Köhler, C. Paternal easiRNAs regulate parental genome dosage in Arabidopsis (2018) Nature Genetics, 50 (2), pp. 193-198.

Martinez, G., Wolff, P., Wang, Z., Moreno-Romero, J., Santos-González, J., Conze, L.L., Defraia, C., Slotkin, R.K., Köhler, C. Paternal easiRNAs regulate parental genome dosage in Arabidopsis (2018) Nature Genetics, 50 (2), pp. 193-198. DOI: 10.1038/s41588-017-0033-4

Slotkin, R.K. The case for not masking away repetitive DNA (2018) Mobile DNA, 9 (1), art. no. 15, . DOI: 10.1186/s13100-018-0120-9

Daron, J., Slotkin, R.K. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels (2017) Genome Biology, 18 (1), art. no. 91.

Martinez, G., Choudury, S.G., Slotkin, R.K. tRNA-derived small RNAs target transposable element transcripts (2017) Nucleic Acids Research, 45 (9), pp. 5142-5152.

Daron, J., Slotkin, R.K. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels (2017) Genome Biology, 18 (1), art. no. 91.

Panda, K., Ji, L., Neumann, D.A., Daron, J., Schmitz, R.J., Slotkin, R.K. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation (2016) Genome Biology, 17 (1), art. no. 170.

Martínez, G., Panda, K., Köhler, C., Slotkin, R.K. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell (2016) Nature Plants, 2 (4), art. no. 16030.

McCue, A.D., Panda, K., Nuthikattu, S., Choudury, S.G., Thomas, E.N., Slotkin, R.K. ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation (2015) EMBO Journal, 34 (1), pp. 20-35.

Nuthikattu, S., McCue, A.D., Panda, K., Fultz, D., DeFraia, C., Thomas, E.N., Keith Slotkin, R. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs (2013) Plant Physiology, 162 (1), pp. 116-131.

McCue, A.D., Nuthikattu, S., Slotkin, R.K. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs (2013) RNA Biology, 10 (8), pp. 1379-1395.

McCue, A.D., Nuthikattu, S., Reeder, S.H., Slotkin, R.K. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA (2012) PLoS Genetics, 8 (2), art. no. e1002474.

Borges, F., Gardner, R., Lopes, T., Calarco, J.P., Boavida, L.C., Slotkin, R.K., Martienssen, R.A., Becker, J.D. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei (2012) Plant Methods, 8 (1), art. no. 44.

Borges, F., Pereira, P.A., Slotkin, R.K., Martienssen, R.A., Becker, J.D. MicroRNA activity in the Arabidopsis male germline (2011) Journal of Experimental Botany, 62 (5), pp. 1611-1620.

Jiang, N., Ferguson, A.A., Slotkin, R.K., Lisch, D. Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition (2011) Proceedings of the National Academy of Sciences of the United States of America, 108 (4), pp. 1537-1542.

Olmedo-Monfil, V., Durán-Figueroa, N., Arteaga-Vázquez, M., Demesa-Arévalo, E., Autran, D., Grimanelli, D., Slotkin, R.K., Martienssen, R.A., Vielle-Calzada, J.-P. Control of female gamete formation by a small RNA pathway in Arabidopsis (2010) Nature, 464 (7288), pp. 628-632.

Slotkin, R.K., Vaughn, M., Borges, F., Tanurdžić, M., Becker, J.D., Feijó, J.A., Martienssen, R.A. Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen (2009) Cell, 136 (3), pp. 461-472.

Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C., Shiu, S.-H., Jiang, N. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile (2009) Plant Cell, 21 (1), pp. 25-38.

Gruntman, E., Qi, Y., Slotkin, R.K., Roeder, T., Martienssen, R.A., Sachidanandam, R. Kismeth: Analyzer of plant methylation states through bisulfite sequencing (2008) BMC Bioinformatics, 9, art. no. 371.

Tanurdzic, M., Vaughn, M.W., Jiang, H., Lee, T.J., Slotkin, R.K., Sosinski, B., Thompson, W.F., Doerge, R.W., Martienssen, R.A. Epigenomic consequences of immortalized plant cell suspension culture. (2008) PLoS biology, 6 (12).

Slotkin, R.K., Freeling, M., Lisch, D. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication (2005) Nature Genetics, 37 (6), pp. 641-644.

Slotkin, R.K., Freeling, M., Lisch, D. Mu killer Causes the Heritable Inactivation of the Mutator Family of Transposable Elements in Zea mays (2003) Genetics, 165 (2), pp. 781-797.

Honors & Awards

Selected honors and awards

Kavli Frontiers of Science Fellow, U.S. National Academy of Science 2013

Early Career Award, American Society of Plant Biologists 2010