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.

转座因子（TEs）定期捕获基因片段。当宿主使这些TE沉默时，与捕获区域同源的siRNA也可能靶向该基因。这种表观遗传的串扰建立了基因组内冲突：使TE沉默需要付出使基因沉默的代价。但是，如果基因很重要，自然选择可以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，我们重点研究了玉米基因组中的Helitrons，Pack-MULEs和Sirevirus LTR反转录转座子这一模型。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，供体基因比没有捕获证据的基因定位更多的siRNA，甲基化程度更高。但是，这些模式在Syntelog和易位供体基因之间有所不同。通过基因表达测量，Syntelog似乎可以维持功能，这与功能重要基因的沉默减缓相一致。表观遗传标记未扩散到其捕获区域以外，并且24nt串扰siRNA与CHH甲基化相关。相反，易位基因具有沉默的特征。它们被高度甲基化并且表达较少，但是在供体基因中也存在过多，并且远离染色体臂，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为潜在的功能类别，支持了基于协同的发现。TE家族以不同的方式捕获基因，但是其优势的证据通常不太明显。但是，带有捕获片段的TE较旧，定位的siRNA较少，与未捕获片段的TE相比，甲基化程度略低。总的来说，我们的结果认为TE捕获触发了内部基因组冲突，该冲突可能不会影响重要基因的功能，但可能导致约束较少的基因的假基因化。