Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
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DOI：
10.1093/genetics/iyaa003
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发表时间：
2021-01-01
期刊：
影响因子：
3.3
通讯作者：
Springer, Nathan M.
中科院分区：
文献类型：
--
作者：
Noshay, Jaclyn M.;Marand, Alexandre P.;Springer, Nathan M.
转座因子（TE）具有通过破坏现有DNA调控元件和通过创建新的DNA调控元件来创建调控变异的潜力。在具有大基因组的物种中，例如玉米，由于个体之间的TE存在/不存在多态性，散布有基因的许多TE为显著的等位基因变异创造了机会。我们使用的信息，推定的调控元件结合知识TE多态性在玉米中，以确定TE插入中断现有的可访问的染色质区域（ACR）在B73以及多态性TE的例子，包含ACR之间的四个玉米自交系，包括B73，Mo 17，W22，PH 207。在其他三个组装的玉米基因组（Mo 17、W22或PH 207）中的TE插入中断了B73基因组中存在的ACR，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。近20%的ACR位于距离最近的基因超过2kb的位置，位于注释的TE内。这些是未甲基化DNA的区域，其显示出类似于TE中不存在的ACR的功能重要性的证据。使用大量的玉米基因型，我们测试了中断或携带ACR的TE插入的存在与附近基因的表达之间是否存在关联。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表现出与附近基因的更高表达相关的富集，这表明这些TE可能有助于新的调控元件。这些分析强调了TE的子集在真核基因组中重新连接转录反应的潜力。
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.