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ripening transcription factors on promoter
cytosine methylation of numerous
ripening-related genes also suggests their
participation in methylation dynamics.
Previously described tomato fruit-
expressing methyltransferases (Teyssier
et al.
, 2008) may contribute to these
methylation patterns in addition to
demethylases. Additionally, these dif-
ferentially methylated regions (DMRs)
generally did not co-localize with siRNAs
or other sRNAs, suggesting non-sRNA-
mediated methylation control of these loci.
While the localization of DMRs in
promoters of ripening-related genes that
became hypomethylated during fruit
maturation was correlated with ripening,
further evidence for a causal relationship
between epigenome dynamics and ripening
control resulted from analysis of binding of
the RIN protein to many of the same
regions populated with ripening-related
DMRs, as determined by chromatin
immunoprecipitation sequencing analysis
using an antibody to RIN (Zhong
et al.
,
2013). Together, these results indicate that
the dynamics of the epigenome provides a
layer of regulatory oversight over a
developmental process. Whether this
represents an avenue towards increased
regulatory stringency over a process that
would be highly detrimental if not lethal in
the wrong tissue or stage of development,
or a common phenomenon that remains to
be elucidated in additional species and
developmental programmes, remains to be
determined. In addition, the fact that
inhibitor-induced hypomethylation induced
premature ripening and that ripening
transcription factors inhibited demethyl-
ation suggest a system of regulatory
feedback between ripening transcription
factors and cytosine methylation processes
that remains to be fully understood, and
that may provide a regulatory model for
additional control systems (see Plate 8).
the response to both abiotic and biotic
stresses. Both cytosine methylation and
histone acetylation can mediate the
pathogen response of
Arabidopsis
to
Pseudomonas syringae
infection (Wang
et
al.
, 2013), and descendents of similarly
infected
Arabidopsis
plants were more
capable of mounting a defensive response
to subsequent infections of
Pseudomonas
or additional pathogens (Slaughter
et al.
,
2012). Dowen
et al.
(2012) observed that
Arabidopsis
methylation mutants were
more resistant to
Pseudomonas
infection
and performed whole-genome surveys of
cytosine methylation in
Arabidopsis
plants
subject to either virulent or avirulent
Pseudomonas
inoculation or salicylic acid
defence hormone treatment. All treatments
resulted in changes in DNA methylation
patterns, often in transposon repeats
adjacent to genes. These genes frequently
displayed differential gene expression
profi les compared with untreated controls,
and the differentially methylated tran-
sposon sequences were also shown to have
corresponding differences in siRNA
accumulation. Together, these results
indicate that pathogen attack infl uences
specifi c gene activities through epigenome
modifi cations, specifi cally variation in
cytosine methylation of transposons via
siRNAs and probably via hormone-
mediated mechanisms. The parallels to
fruit sex determination in melon described
above, which also includes hormone
(ethylene) and DNA methylation processes,
suggest common pathways for utilizing
epigenome dynamics to mediate useful
gene expression responses.
17.4 Challenges and Opportunities
The epigenome clearly provides additional
context and information beyond that
harboured within the DNA sequence code.
Recent studies have provided broad
insights into methods of RNA-mediated
cytosine methylation and mechanisms for
histone covalent modifi cations that change
the functional attributes of associated DNA
sequences. As sessile organisms, plants, in
17.3.3 Response to stress
In addition to developmental effects, the
epigenome has been shown to infl uence
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