DNA demethylation: a lesson from the garden - PubMed (original) (raw)

Review

DNA demethylation: a lesson from the garden

Yoko Ikeda et al. Chromosoma. 2009 Feb.

Abstract

Gene silencing by DNA methylation is well documented and known to be essential for various biological phenomena in many organisms. In contrast, the processes that convert the silent state of a gene whose DNA is methylated and predicted to form facultative heterochromatin to the actively transcribed state remain elusive. In Arabidopsis, recent studies have shown that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING1 (ROS1) participate in DNA demethylation. DME is necessary for genomic imprinting in the endosperm, while ROS1 is involved in pruning DNA methylation patterns in transposons and genic regions of vegetative tissues. These findings provide us with molecular clues for understanding the underlying mechanisms of DNA demethylation and gene activation. In this review, we will consider and discuss the processes of controlling gene activation through DNA demethylation, which are predicted to include the recognition of target sequences, DNA demethylation, the transformation of the chromatin to the active state, and transcription. Many of these processes remain poorly understood at this stage.

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References

1. 1. Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R47-58 - PubMed
2. 1. J Biol Chem. 1995 Apr 28;270(17):9734-9 - PubMed
3. 1. Cell. 2002 Dec 13;111(6):803-14 - PubMed
4. 1. Science. 2008 Jan 25;319(5862):462-5 - PubMed
5. 1. Plant Mol Biol. 2007 Jul;64(4):387-95 - PubMed

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