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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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variation and parent-of-origin effect (Eichten et al.,
2011; Waters et al., 2011) owing to its large endosperm.
Genetically, maize is a highly diverse species (Buckler
et al., 2006; Messing and Dooner, 2006) and has
complex genome organization with many interspersed
genic and repetitive regions (Rabinowicz and Bennet-
zen, 2006; Schnable et al., 2009). Imprinted genes are
arranged in singletons in Arabidopsis and Rice
(Gehring et al., 2011; Luo et al., 2011; Wolff et al.,
2011) but gene clusters are relatively more frequent in
maize (Zhang et al., 2011), in contrast, in mammals,
they are found in clusters (Kinoshita, 2004; Gutierrez-
Marcos et al., 2006; Jullien, 2006; Feil and Berger,
2007). Imprinted gene expression is classified as
paternal imprinting (PEG) or maternal imprinting
(MEG) depending upon which parental allele is
expressed, allele-specific imprinting (certain alleles at
a given locus are imprinted) or gene-specific imprinting
(all the alleles at a given locus are imprinted), binary
imprinting (monoallelic expression where only one of
the parental allele is expressed and other is silent) or
differential imprinting (biallelic expression where both
alleles are expressed but in different quantities) and
constitutive- and transient-imprinted genes depending
on the duration of imprinting (Springer and Gutierrez-
Marcos, 2009). Imprinting was first reported for R
locus in maize which is responsible for aleurone
pigmentation of the maize kernel, such as R-r:
standard (R-r:std) wherein maize produced fully
colored kernel when inherited from female and
mottled kernels when paternally inhererited (Kermicle,
1970; Kermicle, 1978; Kermicle and Alleman, 1978;
MacDonald, 2012). Although genetic imprinting was
first discovered in maize, so far there are only few
gene-specific imprinted genes reported in maize
(including
Fie1
,
Fie2
,
Peg1
,
Nrp1
,
Mez1
,
Meg1
, and
Mee1
), most of which are preferentially expressed
in the endosperm. All except Peg1 show maternal-
specific expression (Zhang et al., 2011). Recent ad-
vances in transcriptome profiling techniques like deep
sequencing have reported many PEGs and MEGs in
Maize endosperm (Waters et al., 2011).
1 Epigenetic mechanisms
Chromatin level of genome activity is controlled at
various levels of DNA and histone modifications
(Roudier et al., 2011). Covalent modifications of
histones, DNA methylation, incorporation of histone
variants, and other factors, such as chromatin-remode-
lling enzymes or small RNAs, all contribute to
defining distinct chromatin states that modulate access
to DNA (Berger, 2007; Kouzarides, 2007; Roudier et
al, 2011). The different epigenetic mechanisms include:
a. Modification at the DNA level (Cytosine methy-
lation); b. Modifications at protein level - the histone
code (Histone acetylation; Histone methylation; His-
tone phosphorylation; Histone ubiquitination; Different
types of histones); c. Chromatin remodeling - chromatin
remodeling proteins.
2 DNA methylation
Methylation patterns of the cytosine residues in the
CpG islands serve as one of the important source code
in regulating gene expression in epigenetic mechanism.
CpG island is a stretch of DNA sequence with high
frequency of CpG occurrence and C + G content of
more than 50% (Gardiner-Garden and Frommer, 1987;
Takai and Jones, 2002) and most commonly observed
near promoter regions (Bird et al., 1995). Hyperme-
thylation of DNA in CpG islands is associated with
the maintenance of gene suppression, while hypo-
methylation in these regions is associated with gene
expression (Biermann and Steger, 2007). DNA methy-
lation is regulated by DNA methyltransferases that
transfer methyl groups from S-adenosyl-methionine
to 5' position of cytosine residues of CpG island
(Biermann and Steger, 2007). In plants, DNA methy-
lation occurs at cytosine residues in CG, CHG and
CHH different sequence contexts (Law and Jacobsen,
2010). Unlike DNMT1 which is involved in maintai-
ning established methylation patterns and DNMT3A
and DNMT3B in de novo methylation patterns in
mammals (Bestor et al., 1988; Lei et al., 1996; Okano
et al., 1999; Singh et al., 2011). Maintenance is carried
out by DNA methyltransferase 1 (MET1), variant in
methylation (VIM) and decreased DNA methylation 1
(DDM1) (at CG sites), chromomethylase 3 (CMT3)
(CHG and CHH) and to some extent de novo CHG
methylation is established by domains rearranged
methyltransferase 2 (DRM2) in plants (Law and Jaco-
bsen, 2010; Wollmann and Berger, 2012). Twenty-four
nucleotide long (24 nt) small interfering RNAs