Supplemental Material for Noshay et al., 2020

Transposable elements (TEs) have the potential to create regulatory variation both through disruption of existing DNA regulatory elements and through creation of novel DNA regulatory elements. In a species with a large genome, such as maize, the many TEs interspersed with genes creates opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22 or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes the TEs that carry ACRs exhibit an enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.

转座因子（Transposable elements, TEs）既可通过破坏现存DNA调控元件，也可通过构建全新DNA调控元件，进而产生调控变异。对于基因组庞大的玉米这类物种而言，大量散布于基因之间的转座因子，会因个体间转座因子的有无多态性，带来显著的等位基因变异契机。我们结合玉米中推定调控元件的相关信息与转座因子多态性的已知特征，鉴定出两类转座因子插入事件：一类是打断B73基因组内现存开放染色质区域（accessible chromatin regions, ACRs）的插入事件，另一类是在B73、Mo17、W22与PH207这四个玉米近交系中，携带开放染色质区域的多态性转座因子实例。其余三个已组装完成的玉米基因组（Mo17、W22或PH207）中，那些打断B73基因组内现存开放染色质区域的转座因子插入事件，可引发染色质结构改变，暗示这类插入事件同时具备遗传与表观遗传层面的潜在影响。在距离最近基因超过2kb的开放染色质区域中，近20%的区域位于已注释的转座因子内部。这类区域属于未甲基化DNA区域，其功能重要性的相关证据与未位于转座因子内的开放染色质区域相似。我们借助大型玉米基因型研究群体，检验了打断或携带开放染色质区域的转座因子插入事件与邻近基因表达水平之间是否存在关联。尽管多数转座因子多态性与邻近基因的表达并无关联，但携带开放染色质区域的转座因子，却显著富集于与邻近基因高表达相关的类别中，这表明这类转座因子或许能够贡献全新的调控元件。本研究的分析结果凸显了部分转座因子具备重塑真核基因组转录响应的潜力。