Spreading of heterochromatin is limited to specific families of maize retrotransposons.
Spreading of heterochromatin is limited to specific families of maize retrotransposons.
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DOI：
10.1371/journal.pgen.1003127
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Springer NM
中科院分区：
文献类型：
--
作者：
Eichten SR;Ellis NA;Makarevitch I;Yeh CT;Gent JI;Guo L;McGinnis KM;Zhang X;Schnable PS;Vaughn MW;Dawe RK;Springer NM
转座因子（te）具有作为影响基因表达的控制因子的潜力，并且经常受到异色沉默的影响。目前的研究表明，异染色质沉默可以扩散到te之外，并影响邻近低拷贝序列的染色质状态。这将允许te对强制性或便利的外部性进行调节，并充当控制要素。玉米基因组包含许多I类te（反转录转座子）家族，它们以中等到高拷贝数存在，并且许多家族位于基因附近的区域，这为测试反转录转座子的异染色质扩散是否普遍提供了机会。我们通过分析玉米基因组低拷贝区组蛋白3赖氨酸9 （H3K9me2）的DNA甲基化和二甲基化，研究了异染色质向每个反转录转座子家族两侧DNA扩散的程度。不同的反转录转座子家族对局部染色质的影响是高度可变的。一些反转录转座子家族在800 - 1200个碱基对插入位点内表现出异色标记的富集，而其他家族则表现出很少的异色标记扩散的证据。对缺乏特异性插入的基因型中染色质状态的分析表明，低拷贝DNA侧反转录转座子中的异染色质通常是由沉默标记的扩散而不是插入位点偏好引起的。位于te附近表现出异染色质扩散的基因往往比其他基因表达水平低。我们的研究结果表明，一部分反转录转座子家族可能是影响邻近序列的控制元件，而大多数反转录转座子对侧翼序列的影响很小。转座因子构成了许多真核生物基因组的重要部分。这些可移动的DNA片段可以通过插入编码区直接导致基因突变，但也可能通过附近的插入影响基因调控。有证据表明，大多数转座因子是表观遗传沉默的，在某些情况下，这种沉默可能会传播到邻近的序列。这种异染色质的扩散可能会在转座子沉默和基因表达之间产生显著的适应性权衡。玉米基因组具有复杂的组织结构，许多基因两侧都有反转录转座子，这为研究反转录转座子与基因的相互作用提供了机会。为了调查与不同反转录转座子家族相关的异染色质扩散的流行程度，我们分析了150个高拷贝反转录转座子家族的异染色质在附近低拷贝序列中的扩散情况。虽然许多反转录转座子很少或没有表现出异染色质的扩散，但也有一些反转录转座子家族确实表现出扩散。位于散布异染色质的反转录转座子附近的基因表达水平较低。将异染色质标记传播到附近低拷贝序列的反转录转座子家族可能由于抑制位于插入附近的基因而增加了宿主基因组的适应成本。
Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800–1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences. Transposable elements comprise a substantial portion of many eukaryotic genomes. These mobile fragments of DNA can directly mutate genes through insertions into coding regions but may also affect the gene regulation through nearby insertions. There is evidence that the majority of transposable elements are epigenetically silenced, and in some cases this silencing may spread to neighboring sequences. This spreading of heterochromatin could create a significant fitness tradeoff between transposon silencing and gene expression. The maize genome has a complex organization with many genes flanked by retrotransposons, providing an opportunity to study the interaction of retrotransposons and genes. To survey the prevalence of heterochromatin spreading associated with different retrotransposon families, we profiled the spread of heterochromatin into nearby low copy sequences for 150 high copy retrotransposon families. While many retrotransposons exhibit little to no spreading of heterochromatin, there are some retrotransposon families that do exhibit spreading. Genes located near retrotransposons that spread heterochromatin have lower expression levels. The families of retrotransposons that spread heterochromatin marks to nearby low-copy sequences may have increased fitness costs for the host genome due to their suppression of genes located near insertions.
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影响因子：
14.9
作者：
Gent JI;Dong Y;Jiang J;Dawe RK
通讯作者：
Dawe RK
DOI：
10.1073/pnas.132259199
发表时间：
2002-07-09
影响因子：
11.1
作者：
Fu, HH;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
11.6
作者：
Dorweiler, JE;Carey, CC;Chandler, VL
通讯作者：
Chandler, VL
DOI：
10.1073/pnas.1018222108
发表时间：
2011-02-08
影响因子：
11.1
作者：
Hollister, Jesse D.;Smith, Lisa M.;Gaut, Brandon S.
通讯作者：
Gaut, Brandon S.
影响因子：
7
作者：
Emberton, J;Ma, JX;Bennetzen, JL
通讯作者：
Bennetzen, JL