Biology Reference
In-Depth Information
Responsiveness is likely important for short-term adaptation as it pro-
vides flexible means for large-scale reprogramming of gene expression.
Yet, this creates challenges with respect to the preservation of long-term
epigenetic memory. While stresses can modify chromatin organization
and regulation, the epigenome returns rapidly to a basal state once the stress
is relieved (
Pecinka et al., 2010; Tittel-Elmer et al., 2010
). Interestingly,
stress-induced relaxation of chromatin states affects nucleosome structure
but leaves DNA methylation patterns largely unchanged. This suggests that
DNA methylation might provide a source of stable information for
reestablishing basal chromatin states during recovery.
In plants, cytosine methylation is not restricted to CG sites but also
occurs at CHG and CHH sites. The molecular mechanisms that shape
DNA methylation patterns are well understood, thanks to the ability of
plants to withstand dramatically altered methylomes. At least three families
of DNA methyltransferases (DNMTs) are responsible for establishing or
maintaining cytosine methylation (Reviewed in
Law & Jacobsen, 2010;
Teixeira & Colot, 2010
). DOMAINS REARRANGED METHYL
TRANSFERASE2 (DRM2), a homologue of mammalian DNMT3, is
the main
de novo
DNMT and affects all sequence contexts (
Cao &
Jacobsen, 2002
). DRM2 also plays a role, together with the plant-specific
CHROMOMETHYLTRANSFERASE3 (CMT3), in the maintenance
of methylation at non-CG sites (
Cao et al., 2003
). Along with DRM2,
small interfering RNAs (siRNAs) and proteins of the RNAi pathway are
involved in maintaining methylation at asymmetrical CHH sites via the
so-called RNA-directed DNA methylation (RdDM) pathway (
Huettel
et al., 2007
). CMT3 interacts with H3K9me2-containing nucleosomes
and methylates CHG sites preferentially. METHYLTRANSFERASE1,
the homologue of mammalian DNMT1, is involved in maintaining CG
methylation. Several additional DNMTs are present in the
Arabidopsis
genome, but their functions are unclear (
Cao et al., 2000
). DNA methyla-
tion is enzymatically removed by the activity of methylcytosine DNA
glycosylases, four of which are present in
Arabidopsis
and named REPRES-
SOR OF SILENCING1, DEMETER (DME), DEMETER-LIKE2 and 3
(Reviewed in
Law & Jacobsen, 2010; Teixeira & Colot, 2010
).
Arabidopsis
is the first organism for which a whole-genome single-
nucleotide resolution methylome was extensively characterized (
Cokus
et al., 2008; Lister et al., 2008
). Patterns of DNA methylation differ substan-
tially between genes and transposable elements (TEs) or other repeated
sequences (Reviewed in
Saze & Kakutani, 2011
). Within repeats, which
