Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

Abstract

Cis-regulatory modules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF to control gene expression in specific cellular contexts. Transposable elements (TEs) are uniquely equipped to deposit their regulatory sequences across a genome, which could also contain cis-regulatory modules that coordinate the control of multiple genes with the same regulatory logic. We provide the first evidence of mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs). The majority (77%) of the individual TEs tested exhibited enhancer activity in mouse ESCs. By mutating individual TF-binding sites within the TE, we identified a module of TF-binding motifs that cooperatively enhanced gene expression. Interestingly, we also observed the same motif module in the in silico constructed ancestral TE that also acted cooperatively to enhance gene expression. Our results suggest that ancestral TE insertions might have brought in cis-regulatory modules into the mouse genome.

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells

“…Similar results were obtained for TSC enhancers (Supplementary Figure 2), in line with previous work (Chuong et al 2013). These results suggest that TE+ enhancers are particularly optimised for activity within their respective early embryonic tissues, possibly through the synergistic action of multiple TF binding events (Sundaram et al 2017). Co-option of TE+ enhancers may therefore particularly benefit genes that require highly tissue-specific expression.…”

“…For example, whilst SOX2 binding motifs were present in nearly all (81-91%) RLTR13D6 and RLTR9E TE+ enhancers, a high proportion (48-58%) of nonenhancer TEs also contained this motif. Notably, motifs for other TFs (ESRRB, KLF4) that have been shown to cooperate with SOX2 for RLTR9E enhancer activity (Sundaram et al 2017) were present in similar abundance at both enhancer and nonenhancer TEs (Figure 2A). We then asked whether TF binding motifs predicted plasmid-based enhancer activity better than they predict enhancer-like chromatin profiles.…”

“…TE enhancer activity cannot be faithfully predicted from TF binding motifs Despite their sequence similarity, only a relatively small fraction of TEs from any given subfamily bear enhancer-like profiles. It was previously suggested that TE enhancer activity in the ESC and TSC contexts is determined by the presence of key TF binding motifs, which have otherwise been mutated in inactive TEs (Chuong et al 2013;Sundaram et al 2017). However, it remains unclear whether such motifs are fully determinant of TE enhancer activity.…”

“…We also selected an element interacting with Smarcad1, a gene involved in pluripotency maintenance! (Hong et al 2009), and one element that was previously shown to regulate Akap12 in ESCs (Sundaram et al 2017). After genetically excising TE+ enhancers using pairs of sgRNAs ( Figure 4D) in multiple clones, we measured the effects on the expression of target genes.…”

Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

“…TEs can be a source of cis-regulatory elements that can influence gene regulation (29)(30)(31)(32). For example, TEs have been shown to add transcription factor binding sites, and transcription start sites, leading to changes in expression of nearby genes (33)(34)(35)(36). TEs can also influence gene expression by inducing changes in the chromatin structure (37)(38)(39).…”