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Maize Genomics and Genetics 2012, Vol.3, No.3, 13
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ISSN 1925-1971 http://mgg.sophiapublisher.com
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(siRNAs) have shown to mediate De novo DNA
methylation through the RNA-directed DNA methy-
lation (RdDM) pathway (Simon and Meyers, 2010).
The DNA glycosylase DEMETER (DME) actively
removes DNA methylation (Choi et al., 2002; Kino-
shita et al., 2004) and might contribute to the derepre-
ssion of genes (Wollmann and Berger, 2012). DNA
demethylation can also occur passively in the absence
of enzymes involved in methylation maintenance
process (Hauser et al., 2011). In plant endosperm and
mammalian embryo, many differentially methylated
regions (DMR) are present in the Imprint Control
Regions (ICR) that has critical role in epigenetic
regulation of imprinted domains (Mac-Donald, 2011).
The methylation pattern of these DMRs are erased
in germline, re-established during gametogenesis and
maintained throughout the development and lifecycle.
Further, DNA methylation is coordinated by the
position and composition of nucleosomes and asso-
ciated histone modifications at genome level (Hauser
et al., 2011).
3 Histone modification
The chromatin is made up of nucleosome unit, which
is composed of 146 bp and wrapped around an
octamer of core histones (H2A, H2B, H3 and H4) and
linked by H1. The chemical modifications of the
amino acid residue present in the N-terminal tail
of these histones result in the regulation of the genes.
The modifications viz., methylation, acetylation, phos-
phorylation, ubiquitylation and sumoylation at the
histone tails constitute histone code (Peterson and
Laniel, 2004). There are eight common histone
modifications that are associated with active or
repressed transcriptional state of chromatin (Huan and
Springer, 2008). Modifications of histones H3 and H4,
especially acetylation and methylation of histone
lysine residues at N-terminal tails that protrude from
the nucleosome are best understood in terms of gene
regulation (Hauser et al., 2011). Histone methylation
is the most prominent of the post-translational
modification and is monitored by the histone methyl-
transferases (HMTs). HMTs are involved in either
addition or deletion of one or two methyl groups from
arginine and lysine residues (Singh et al., 2011).
Histone methylation is most commonly associated
with the gene silencing, methylation of H3K9 is found
in heterochromatin and silenced promoters (Fischle et
al., 2003), but it may also associate with gene
activation as in histone H3K4 dimethylation in
maternal allele of maize
Mez1
and
ZmFie1
(Huan and
Springer, 2008). Therefore, methylation of Lys9 and
Lys27 of histone H3 (H3K9 and H3K27) are linked to
heterochromatin and gene silencing, while methy-
lation of Lys4 (H3K4) is linked to transcriptional
activity (Grewal and Elgin, 2002; McDonald, 2011).
Lysine methyltransferase, G9a, is involved in mono-
and dimethylation of H3K9 in euchromatin (Tachi-
bana et al., 2007) while LSD1 and JmjC-domain-
containing proteins are methyltransferases with lysine
demethylase activity that interact with chromatin
remodeling proteins to affect chromatin condensation
(Okada et al., 2007).
Acetylation is the second most important posttrans-
lational histone modification that has antagonistic
role to DNA methylation. Increased histone ace-
tylation at lysine residues is mediated by histone
acetyl transferases (HATs) signifies active genes and
deacetylation through histone deacetylases (HDACs)
inhibit gene expression (Singh et al., 2011). The
mouse
Gtl2
DMR of the silent paternal allele is
hypoacetylated on H3 and H4, while the active
maternal allele carries high levels of acetylation on
both histones (Carr et al., 2007). MYST1, a MYST
family protein is a acetyl transferase (HAT), which
acetylates H3K16 to impact chromatin architecture
(Neal et al., 2000) while SIRT1 is a deacetylase
(HDAC) that removes acetyl groups from H1, H3 and
H4 (Yi and Luo, 2010). Phosphorylation of histones at
serine and threonine residues and ubiquitylation of
lysine residues are associated with either activation or
repression of gene depending on the context. For
example, phosphorylation is usually associated with
gene activation but gene silencing is seen when the
histone variant H2AX is phosphorylated (Fernandez-
Capetillo, 2003) and ubiquitylation of histone H2A is
linked to gene silencing (Baarends et al., 2003)
whereas ubiquitylation of H2B is linked to gene
activation (Zhu et al., 2005). Attachment of small
ubiquitin-related modifier proteins, termed as su-
moylation is yet another process of posttranslational