Gene capture by transposable elements leads to epigenetic conflict in maize
Gene capture by transposable elements leads to epigenetic conflict in maize
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DOI：
10.1016/j.molp.2020.11.003
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发表时间：
2021-02-01
期刊：
影响因子：
27.5
通讯作者：
Bousios, Alexandros
中科院分区：
文献类型：
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作者：
Muyle, Aline;Seymour, Danelle;Bousios, Alexandros
转座因子（Transposable elements，TE）是一种有规律的捕获基因片段的基因。当宿主沉默这些TE时，与捕获区域同源的siRNA也可以靶向基因。这种表观遗传串扰建立了基因组内的冲突：沉默TE的代价是沉默基因。然而，如果基因是重要的，自然选择可能通过调节沉默反应来维持功能，这也可能有利于TE。在这项研究中，我们通过关注玉米基因组中的Helitrons，Pack-MULE和Sirevirus LTR逆转录转座子来研究这个模型。我们记录了1263个TE，其中包含来自1629个供体基因的外显子片段。与表观遗传冲突一致，供体基因映射了更多的siRNA，并且比没有捕获证据的基因甲基化程度更高。然而，这些模式之间的syntelog与易位供体基因不同。Syntelogs似乎保持功能，如通过基因表达所测量的，与功能重要基因沉默的适度一致。表观遗传标记没有扩散到它们捕获的区域之外，并且24 nt串扰siRNA与CHH甲基化相关联。相反，易位的基因带有沉默的特征。它们高度甲基化，表达较少，但在供体基因中也过度表达，并远离染色体臂，这表明捕获和基因运动之间存在联系。基于进化约束将基因分成潜在的功能类别支持了基于同线性的发现。TE家族以不同的方式捕获基因，但其优势的证据通常不太明显;然而，具有捕获片段的TE较老，映射较少的siRNA，并且甲基化程度略低于没有捕获片段的TE。总的来说，我们的研究结果认为，TE捕获触发基因组内的冲突，可能不会影响重要基因的功能，但可能会导致少约束基因的假基因化。
Transposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.