Antagonistic H3K79me-H3K9ac crosstalk determines elongation at housekeeping genes to promote pluripotency

Abstract

Pluripotent embryonic stem cells (ESCs) have a transcriptionally permissive chromatin environment enriched for gene activation-associated histone modifications as compared to somatic cells. A striking exception is DOT1L-mediated H3K79 methylation that is considered a positive regulator of transcription. Here we find that ESCs maintain low H3K79 methylation to facilitate RNA polymerase II (RNAPII) elongation for greater nascent transcription. Inhibiting DOT1L during the reprogramming of somatic to induced pluripotent stem cells (iPSCs) enables ESC-like RNAPII and transcriptional status. Mechanistically, DOT1L inhibition causes a local gain of histone acetylation at genes that lose the most H3K79me, which unexpectedly are ubiquitously expressed genes that perform essential functions in every cell, rather than lineage specifying genes. Maintenance of this elevated histone acetylation is required for the enhanced conversion to iPSCs upon DOT1L inhibition. Remarkably, increasing global DOT1L or site-specific tethering of DOT1L is sufficient to decrease H3K9ac in ESCs. We discover a high H3ac- low H3K79me epigenetic mechanism that promotes transcription elongation at ubiquitously expressed genes to enforce pluripotent cell identity.

DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity

“…A. Expression of DOT1L associated factors determined by bulk RNA-Seq (Wille and Sridharan, 2022) in MEFs, day 2 of reprogramming, day 4 of reprogramming, and ESCs measured as transcripts per million (TPM).…”

“…These changes occur especially at highly expressed housekeeping genes (Fig 5, S4). Compared to somatic cells, ESCs have both a lower TSS-enrichment of RNAPII (Fig 5I) and H3K79me2 (Fig 5G) to mitigate negative transcriptional feedback (Fig 6) (Wille et al, 2022). ESCs have a much greater need for biosynthetic output than somatic cells (Bulut-Karslioglu et al, 2018; Percharde et al, 2017) and are likely to regulate transcription of housekeeping gene in a distinct manner (Wille et al, 2022).…”

“…Compared to somatic cells, ESCs have both a lower TSS-enrichment of RNAPII (Fig 5I) and H3K79me2 (Fig 5G) to mitigate negative transcriptional feedback (Fig 6) (Wille et al, 2022). ESCs have a much greater need for biosynthetic output than somatic cells (Bulut-Karslioglu et al, 2018; Percharde et al, 2017) and are likely to regulate transcription of housekeeping gene in a distinct manner (Wille et al, 2022). Taken together, our data support a negative transcriptional feedback model for AF10 mediated enhancement of DOT1L catalytic activity in the maintenance of cell identity (Fig 6).…”

“…DOT1L has been shown to interact with the phosphorylated C-terminal tail of RNAPII (Kim et al, 2012) and methylates genes concurrent with active transcription (Steger et al, 2008). (Wille et al, 2022). ESCs have a much greater need for biosynthetic output than somatic cells (Bulut-Karslioglu et al, 2018;Percharde et al, 2017) and are likely to regulate transcription of housekeeping gene in a distinct manner (Wille et al, 2022).…”

DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity

“…Because reprogramming is the conversion from the somatic to the pluripotent state, we assessed how many of the H3K79me1/2 genes in the fl and ΔAF10 were modified in MEFs and ESCs. We have previously shown that ∼80% of the H3K79me1/2 locations are shared between MEFs and ESCs ( Wille et al., 2022 ). The vast majority of H3K79me1/2-containing genes in reprogramming populations are also modified in both ESCs and MEFs ( Figure 4 F).…”