Characterization of carrot nuclear proteins that exhibit specific binding affinity towards conventional and non-conventional DNA methylation

DNA methylation is associated with transcriptional silencing in vertebrates and plants. In mammals, the effects of methylation are mediated by a famil y of methyl-CpG-binding proteins. In plants the mechanisms by which methyla tion represses transcription are still not clear. In this paper we describe protein factors in carrot nuclear extracts exhibiting specific affinities for conventional or non-conventional methylation acceptor sites. We charact erized two classes of proteins: the first, dcMBP1 (Daucus carota methylated DNA-binding protein 1), shows high affinity for sequences containing 5-met hylcytosine; the second, dcMBP2 (Daucus carota methylated DNA-binding prote in 2), efficiently complexes sequences containing 5-methylcytosine in both CpXpX and CpXpG trinucleotides and shows much lower affinity for 5-methyl C pG dinucleotides. Both dcMBP1 and dcMBP2 are abundant proteins differing in molecular weight and binding features. Their activities are modulated duri ng carrot vegetative cell growth and somatic embryo development. This is th e first time that, in either plants or mammals, proteins exhibiting specifi c binding affinities for conventional or non-conventional DNA methylation h ave been shown. Based on these results, the possibility that both the exten t and the context of the methylation might contribute to modulate gene expr ession is discussed.