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Professor and HHMI Investigator
Ph.D., Cambridge University, 1986

Plant genetics; transposons; development; gene regulation; DNA methylation

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Martienssen2013 Epigenetic mechanisms of gene regulation impact genome organizationand inheritance, as well as the specification and maintenance of cell fate. These mechanisms are conserved and provide an additional layer of nformation superimposed on the genetic code. We are using model plants and fission yeast to investigate epigenetic mechanisms of transposon silencing, gene regulation and germ cell fate via functional genomics and developmental genetics. In fission yeast, we have found that centromeric repeats are transcribed, and are targets of RNA interference (RNAi). Small RNAs derived from these repeats guide histone H3 lysine 9 methylation and heterochromatin formation during DNA replication, providing a mechanism for inheritance of epigenetic marks through the cell cycle. We have demonstrated parallel mechanisms in plants, especially in the germ line, when transposons are activated  by heterochromatin reprogramming to generate mobile small RNA. The same pathway controls germ cell fate, the regulation of meiosis and recognition of transposons in polyploid hybrids. Our research in plant genomics, includes studies on chromatin organization, DNA replication and chromatin dynamics., and we have found that RNA interference played a critical role in the evolution of flowering plants. We are using genomics and RNAi to improve clonal aquatic flowering plants (Lemnaceae) as a potential source of bioenergy.We maintain an efficient system for site-selected transposon mutagenesis inmaize and a collection of gene trap and enhancer trap lines in Arabidopsis (


Selected Publications

Zaratiegui, M., Vaughn, M.W., Irvine, D.V., Goto, D., Watt, S., Bähler, J., Arcangioli, B., and Martienssen, R.A. 2011.CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature 469: 112–115.

Slotkin, R.K., Vaughn, M., Borges, F., Tanurdzić, M., Becker, J.D., Feijó, J.A., and Martienssen, R.A.Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. 2010.Cell. 136: 461–472.

Irvine, D., Zaratiegui, M., Tolia, N.H., Chitwood, D., Goto, D., Vaughn, M., Joshua-Tor, L.,and Martienssen, R.A. 2006. Argonaute slicing is required for heterochromatic silencing andspreading. Science 313: 1134–1137.

Lippman, Z., Gendrel, A.-V., Black, M., Vaughn, M., Dedhia, N., McCombie, W.R., Lavine, K.,Mittal, V., May, B., Kasschau, K., Carrington, J.C., Doerge, R.W., Colot, V., and Martienssen,R.A. 2004. Role of transposable elements in heterochromatin and epigenetic control.Nature 430: 471–476.

Kidner, C.A., and Martienssen, R.A. 2004. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428: 81–84.