Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [ChIP-seq]

Long terminal repeats (LTRs), which comprise promoter and enhancer region of intact endogenous retroviruses (ERVs), are known to be co-opted for fine-tuning host-coding gene expression as cis-regulatory elements. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, a substantial activation of LTRs have been found in human cells after treatment with epigenetic inhibitors. Although LTR12C family had highest relative abundance of transcripts among the de-repressed ERV families, functional consequences of the activated LTR12C for host-coding genes remain uncover due to genome-wide alteration of epigenetic landscape resulting in broad transcriptional changes after the epigenetic inhibitor treatments. Here, we transactivated more than 600 LTR12C elements by using single guide RNA-based dCas9-Suntag-VP64, which is a kind of the site-specific targeting technology CRISPR activation system, with minimal off-target events. Interestingly, most of transactivated LTR12C elements acquired H3K27ac-marked enhancer feature, while 20% of them along with enrichment of H3K4me3-marked promoter feature. The enrichment of H3K4me3 signal was likely brought about by downstream regions of LTR12C, such as internal regions of intact ERV9 or other type of retrotransposons. To investigate hitone modification changes in HEK293T after CRISPRa, we performed ChIP-seq.