TY - JOUR
T1 - Role of transposable elements in heterochromatin and epigenetic control
AU - Lippman, Zachary
AU - Gendrel, Anne Valérie
AU - Black, Michael
AU - Vaughn, Matthew W.
AU - Dedhia, Neilay
AU - McCombie, W. Richard
AU - Lavine, Kimberly
AU - Mittal, Vivek
AU - May, Bruce
AU - Kasschau, Kristin B.
AU - Carrington, James C.
AU - Doerge, Rebecca W.
AU - Colot, Vincent
AU - Martienssen, Rob
N1 - Funding Information:
Acknowledgements We thank E. Richards and our colleagues T. Osborn, L. Comai, J. Chen and J. Birchler for their comments and advice. We also thank P. Rabinowicz for advice on ChIP microarray experiments. V.C. thanks M. Caboche for laboratory space and continuous support. Z.L. is an Arnold and Mabel Beckman graduate fellow in the Watson School of Biological Sciences. A.V.G. is supported by a graduate studentship from the French Ministry of Research. M.V. is a National Science Foundation Bioinformatics postdoctoral fellow. This work was supported by a grant from the NSF Plant Genome Program (to R.W.D. and R.M.), as well as grants from Genopole and the CNRS (to V.C.), grants from NSF and NIH to J. C., and NIH to R.M.
Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2004/7/22
Y1 - 2004/7/22
N2 - Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.
AB - Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.
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U2 - 10.1038/nature02651
DO - 10.1038/nature02651
M3 - Article
C2 - 15269773
AN - SCOPUS:3342927934
VL - 430
SP - 471
EP - 476
JO - Nature
JF - Nature
SN - 0028-0836
IS - 6998
ER -