Insights into Plant Epigenome Dynamics - Fruit Ripening: Physiology, Signalling and Genomics - page 300

aspects of crop genetics and biology. These
discoveries are opening new paths towards
genetic and biological innovation, with
implications relevant to agricultural
improvement and that are certain to be
heavily pursued in coming years. The
present chapter briefl y describes the basic
mechanisms underlying epigenetic regu-
lation with a special focus on the role of
the epigenome in fruit development and
ripening using the tomato as a reference
species.

facilitated recent and in-depth analysis of
the histone landscape and its intricacies in
this model plant system (Roudier et al. ,
2011, and references therein). Characteri-
zation of multiple histone modifi cations
across the Arabidopsis genome revealed a
degree of nucleosome-associated function-
ality beyond euchromatin/heterochromatin
bifurcation, including at least four general
functional domains termed CS1-CS4. CS1
is composed of active genes with enriched
H3K4 and K3K27 methylation, while C2,
C3 and C4 are associated with various
repressed states (Roudier et al. , 2011).
Characterization of histone profi les in
combination with cytosine methylation
and sRNAs provides additional insight into
the fi delity and impact of epigenome
variation on chromatin activity (Luo et al. ,
2013; see below). Few plant genomes are as
complete as that of Arabidopsis , a
necessity for genome-scale epigenome
analyses. Information on the rice genome is
of suffi cient quality to allow similar
analyses, and provides a bridge between
the less repetitive Arabidopsis genome and
the repetitive genomes of many cereals and
other important crop species. Char-
acterization of histone modifi cations in rice
revealed the same H3K4 and H3K27
methylation association with active genes
(Hu et al. , 2012). The ability to determine
the degree to which similar chromatin
states persist in additional plants and with
similar effect will become feasible as high-
quality ordered reference genomes become
available.

17.2 Components of the Epigenome

17.2.1 Histones and their modifi cations

Eukaryotic DNA possesses the conserved
feature of DNA wrapped in 147-base
intervals around nucleosomes comprised
of eight histone proteins - two each of
histones H2A, H2B, H3 and H4. The
ordering of nucleosomes on DNA strands
and the specifi c chemical modifi cations of
histones vary widely and contribute to the
functional characteristics of specifi c DNA
regions along the chromatin (Filion et al. ,
2010). These features are achieved at least
in part through regulating access to DNA
by both general and specifi c mediators of
transcriptional activity (Berger, 2007).
Indeed, specifi c histone modifi cations have
been closely associated with distinct gene
features and activities. For example,
methylation of lysine 9 of H3 (H3K9) and
H3K27 methylation are found pre-
dominantly in regions of the genome popu-
lated by long terminal repeat retroelements
(Zhang et al. , 2007; Bernatavichute et al. ,
2008) but also in the gene bodies of some
expressed genes (Turck et al. , 2007). H3K4
and H3K36 methylation are often associated
with the 5 c and 3 c ends, respectively, of
transcribed genes, while H3K27 methyl-
ation is more generally associated with
genes displaying reduced transcriptional
activity (Oh et al. , 2008). The compact size
and high-quality genome sequence of
Arabidopsis thaliana has, in conjunction
with effi cient immunoprecipitation, tiling
arrays

17.2.2 Cytosine methylation and small
interfering RNAs (siRNAs)

Eukaryotes display a complex array of
sRNA molecules that mediate a range of
functions related to regulation of gene
expression. sRNAs classifi cations include
microRNAs (miRNAs) and siRNAs, the
former derived from DICER or DICER-like
activity upon small RNA hairpins and the
latter from cleavage of long dsRNAs
(Brodersen and Voinnet, 2006). miRNAs
target specifi c genes or gene families via and sequencing technologies,