Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
Department of Genetics, University of Georgia, 120 W Green St, Athens, GA 30602, USA.
Genetics. 2021 Mar 3;217(1):1-13. doi: 10.1093/genetics/iyaa003.
Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create 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 2 kb 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 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.
转座元件 (TEs) 具有通过破坏现有 DNA 调控元件和创建新的 DNA 调控元件来产生调控变异的潜力。在基因组较大的物种中,如玉米,许多与基因交错的 TEs 由于个体之间的 TE 存在/缺失多态性,为显著的等位基因变异创造了机会。我们利用假定的调控元件信息,并结合玉米 TE 多态性的知识,鉴定了在 B73 中中断现有可及染色质区域 (ACRs) 的 TE 插入,以及在包括 B73、Mo17、W22 和 PH207 在内的四个玉米自交系中含有 ACRs 的多态性 TE 示例。在另外三个组装的玉米基因组 (Mo17、W22 或 PH207) 中,中断 B73 基因组中存在的 ACR 的 TE 插入可以触发染色质的变化,这表明这些插入具有遗传和表观遗传影响的潜力。位于距离最近基因 2kb 以上的 ACR 中,近 20%位于注释的 TE 内。这些是未甲基化 DNA 区域,具有与不在 TE 内的 ACR 相似的功能重要性证据。使用大量玉米基因型,我们测试了中断或携带 ACR 的 TE 插入是否与附近基因的表达有关。虽然大多数 TE 多态性与附近基因的表达无关,但携带 ACR 的 TE 表现出与附近基因表达更高相关的富集,这表明这些 TE 可能提供新的调控元件。这些分析强调了一小部分 TEs 有可能重新布线真核生物基因组中的转录反应。