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首页玉米甲基化组学:调控机制与作物改良潜力
玉米甲基化组学:调控机制与作物改良潜力
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《玉米甲基化:基因沉默与表观遗传的新篇章》 本文探讨了玉米(Maize)中的甲基化现象,这是一种在植物中普遍存在的染色质修饰,与基因表达调控密切相关。DNA甲基化通常与基因沉默或异染色质化相联系,通过有丝分裂或减数分裂的稳定遗传机制得以传递。这种特性使得甲基化能够在玉米和其他作物中作为表观遗传信息的载体,影响非序列决定的性状遗传。 表观遗传学关注的是那些可以通过基因组外因素传承的遗传信息,而不单纯依赖于DNA序列本身。玉米是最早被发现表观遗传现象的植物之一,包括参数突变、印记和转座子失活。这些现象都与DNA甲基化有着密切关联。例如,参数突变涉及甲基化模式的改变导致基因表达异常;印记则是指特定染色体上的基因只在父本或母本遗传时甲基化状态不同;而转座子失活则表明DNA甲基化可能在控制转座子活性和染色质状态中扮演关键角色。 随着对拟南芥(Arabidopsis)中调控DNA甲基化的分子机制的深入研究,科学家们已经揭示了一些关键基因和途径。这些发现为理解玉米甲基化的调控网络提供了线索,有助于我们探索如何利用表观遗传变异来改良玉米品种。自然条件下,玉米的不同品系间存在显著的表观遗传状态差异,这可能是作物改良的重要资源,因为它们可以影响植物的生长性状、抗逆性以及其他经济性状。 本文主要讨论了玉米甲基化在植物发育和表观遗传中的核心作用,以及它在玉米育种中的潜在价值。通过理解这些分子机制,科研人员正在努力开发新的育种策略,以利用表观遗传的可塑性来优化玉米的性能,以满足不断增长的人类粮食需求。
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6.3.1 Methylation Domains
in the Maize Genome
Assessing the relative levels of CG, CHG, and
CHH methylation in windows of the maize
genome can be used to define different types of
methylation domains (Springer and Schmitz
2017). The methylation domains include
CG/CHG/CHH regions (RNA-directed DNA
methylation, or RdDM targets), CG/CHG
regions (hete rochromatin), CG only (gene body
methylation—gBM), unmethylated regions, and
unclassified regions with intermediate levels of
DNA methylation (Fig. 6.1). CG/CHG domains,
which contain high levels of CG and CHG
methylation, but very low levels of CHH
methylation, are the most common type in the
maize genome, accounting for large portions of
intergenic and TE regions of the genome but are
less abundant within genes (Fig. 6.1). The
RdDM targets, which have elevated methylation
in all three contexts, only account for 2% of the
maize genome and are most prevalent within
intergenic regions. Regions with only CG
methylation account for *6% of the maize
genome and are often found within maize gene
bodies. Approximately 11% of the maize gen-
ome has low levels of methylation in all three
contexts, and this is most prevalent within the
genic portions of the maize genome and is quite
rare in TEs. Another 10% of the maize genome
has inte rmediate levels of DNA methylation that
are difficult to classify.
6.3.2 DNA Methylation Patterns
at Maize Genes
The distribution of methylation within plant
genomes reflects the distinct methylation profiles
at genes and TEs. In general, CG and CHG
methylation levels are high in non-genic regions
but drop to low levels near the transcription start
site (TSS) and transcription terminat ion site
(TTS) of annotated genes (Regulski et al. 2013;
Gent et al. 2013; West et al. 2014). Within gene
bodies, there are moder ate levels of CG methy-
lation likely reflecting gene body met hylation
(Neiderhuth et al. 2016). Maize also contains
significant levels of CHG methylation in gene
bodies that is partially attributable to methylation
of TEs found within introns (West et al. 2014).
CHH methylation is enriched in regions flanking
maize genes (Gent et al. 2013). These mCHH
islands mark the boundary between high levels of
CG and CHG methylation outside of maize genes
and the reduced levels of methylation in genes
(Li et al. 2015a). Several factors influence the
profile of DNA methylation over maize genes. In
general, highly expressed genes have the lowest
levels of DNA methylation at the TSS and TTS
(Regulski et al. 2013; Gent et al. 2013; West
et al. 2014). However, the inverse pattern is
observed for CHH methylation in regions
upstream of the TSS (Gent et al. 2013). Genes
located in syntenic positions relative to other
grasses exhibit much lower levels of DNA
methylation than inserted (non-syntenic) genes
(Eichten et al. 2011; West et al. 20 14). There is
no evidence for differential levels of DNA
methylation for genes in the two subgenomes
that have resulted from the ancient
whole-genome duplication event in maize
(Eichten et al. 2011; West et al. 2014).
6.3.3 DNA Methylation Patterns
at Maize TEs
DNA methylation at TEs is high relative to
flanking regions (West et al. 2014). The levels of
CG and CHG met hylation over TEs are higher in
maize than in Arabidopsis (West et al. 2014),
with more gradual transitions from low to high
methylation levels at the edges of TEs, suggest-
ing greater spreading of DNA methylation from
TEs to flanking regions in maize (Eichten et al.
2012). The analysis of transposon superfamilies
revealed variation in chromatin profiles (West
et al. 2014). While CG and CHG methylation are
very high for all families, there is variation for
the level of CHH methylat ion and H3K9me2
(West et al. 2014). There is also eviden ce for
family-specific variation in whether DNA
methylation can spread to flanking regions, sug-
gesting that TE families associated with
84 J. M. Noshay et al.
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