Loss of heterochromatin at endogenous retroviruses creates competition for transcription factor binding

Abstract

The mammalian genome is partitioned into active and inactive regions, broadly termed euchromatin and heterochromatin, respectively. The majority of heterochromatin consists of repetitive elements, including endogenous retroviruses (ERVs). ERVs are enriched in regulatory elements containing transcription factor (TF) binding sites with individual families containing hundreds to thousands of distinct copies scattered throughout the genome. We hypothesized that epigenetic derepression of ERVs (such as that observed during early development) may alter the stoichiometry between TFs and their euchromatic target sites, with ERVs effectively competing for these factors. To test this, we modeled acute heterochromatin loss using inducible deletion of the co-repressor KAP1 in mouse embryonic stem cells (ESCs). Upon KAP1 deletion, we observe clear reductions in chromatin accessibility, histone acetylation, and TF binding at euchromatic regions. To directly test the concept of global binding site competition, we designed exogenous binding site arrays (EBSAs) to introduce upwards of 1500 copies of the OCT4 TF binding motif into ESCs. OCT4 EBSAs specifically reduce chromatin accessibility at POU family motifs and result in reduced transcription of the pluripotency machinery with subsequent differentiation. Overall, these data support a model in which heterochromatin at ERVs promotes euchromatic TF binding and transcriptional homoeostasis. We propose that regulated ERV derepression during pre-implantation may serve as a developmental siphon to weaken the robustness of ongoing transcription programs in favor of the plasticity required for cell fate specification.

Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children

“…4b, Fig S7b-d). It has been recently shown that non-repressed ERVs can create competition for TF binding, and in addition, decreased heterochromatin levels at ERVs were associated with overall decreased H3K27ac in other genomic regions [39]. This model ts well with our data in which increased H3K9me3 at ERV sites and increased H3K27ac levels at other sites in the genome are suggesting a deleterious masking of ERV sites.…”

“…To address this, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in 18-week-old children targeting H3 trimethylation on lysine 9 (H3K9me3). H3K9me3 mark is associated with constitutive heterochromatin and has a role in development by repressing lineage inappropriate genes, as well as a role in repressing endogenous retroviruses (ERVs) and other transposable elements (TEs) [36], whose regulatory roles in gene expression are currently being investigated [37][38][39]. Furthermore, animal studies suggest that H3K9me3 plays a crucial role in transgenerational inheritance in response to environmental changes, including nutritional changes [40,41].…”

Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency

“…These findings are consistent with previous studies that have proposed a mechanism of “repression-by-theft”, wherein transient elements mediate the redistribution of somatic TFs away from their somatic targets (Chronis et al ., 2017; Knaupp et al ., 2017). This mechanism is analogous to the silencing of Runx1 targets caused by redistribution of Runx1 upon expression of the pioneer factor SPI1 in T-cell development (Hosokawa et al ., 2018; Deng et al ., 2021), and the loss of pluripotency observed when introducing exogenous OCT4 binding arrays in ESCs (O’Hara and Banaszynski, 2022). The day 1 and 2 multiome analysis revealed a quantitative association between the sequestration of somatic TFs to newly opened sites and the repression of somatic gene expression.…”

The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations

“…The silencing of endogenous TEs in mouse stem cells occurs in part through the recruitment of H3K9-methyltransferase SETDB1 and its co-repressor TRIM28 ( Thompson et al, 2016 ). Loss of TRIM28 and/or SETDB1 not only causes re-activation of TEs, but also leads to reductions in transcriptional activation machinery over euchromatic loci, including decreased histone acetylation and loss of transcription factor binding ( Asimi et al, 2022 ; O'Hara and Banaszynski, 2022 preprint). Most notably, binding of pluripotency factors (Oct4, Sox2 and Nanog) or RNA polymerase II is reduced over their normal genic targets in response to H3K9me3 loss, in favor of ectopic localization at de-repressed TEs.…”