Long terminal repeats (LTRs), which often contain promoter and enhancer sequences of intact endogenous retroviruses (ERVs), are known to be co-opted as cis-regulatory elements for fine-tuning host-coding gene expression. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, substantial activation of LTRs has been found in human cells after treatment with epigenetic inhibitors. Although the LTR12C family makes up the majority of ERVs activated by epigenetic inhibitors, how these epigenetically and transcriptionally activated LTR12C elements can regulate the host-coding gene expression remains unclear due to genome-wide alteration of transcriptional changes after epigenetic inhibitor treatments. Here, we specifically transactivated >600 LTR12C elements by using single guide RNA-based dCas9-SunTag-VP64, a site-specific targeting CRISPR activation (CRISPRa) system, with minimal off-target events. Interestingly, most of the transactivated LTR12C elements acquired the H3K27ac-marked enhancer feature, while only 20% were co-marked with promoter-associated H3K4me3 modifications. The enrichment of the H3K4me3 signal was intricately associated with downstream regions of LTR12C, such as internal regions of intact ERV9 or other types of retrotransposons. Here, we leverage an optimized CRISPRa system to identify two distinct epigenetic signatures that define LTR12C transcriptional activation, which modulate the expression of proximal protein-coding genes.

中文翻译：

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数百个 LTR12C 元件的有效激活揭示了由不同表观遗传机制决定的顺式调节功能


长末端重复序列 (LTR) 通常含有完整内源逆转录病毒 (ERV) 的启动子和增强子序列，已知可作为顺式调控元件来微调宿主编码基因的表达。由于 LTR 主要是通过抑制性表观遗传标记的沉积而沉默，因此在用表观遗传抑制剂处理后，在人类细胞中发现了 LTR 的大量激活。尽管LTR12C家族构成了表观遗传抑制剂激活的大部分ERV，但由于表观遗传抑制剂处理后全基因组转录变化的改变，这些表观遗传和转录激活的LTR12C元件如何调节宿主编码基因表达仍不清楚。在这里，我们通过使用基于单向导 RNA 的 dCas9-SunTag-VP64（一种位点特异性靶向 CRISPR 激活 (CRISPRa) 系统）特异性反式激活 > 600 个 LTR12C 元件，并且脱靶事件最少。有趣的是，大多数反式激活的LTR12C元件获得了H3K27ac标记的增强子特征，而只有20%与启动子相关的H3K4me3修饰共同标记。 H3K4me3 信号的富集与 LTR12C 的下游区域错综复杂地相关，例如完整 ERV9 的内部区域或其他类型的反转录转座子。在这里，我们利用优化的 CRISPRa 系统来识别两个不同的表观遗传特征，这些特征定义了 LTR12C 转录激活，从而调节近端蛋白质编码基因的表达。