Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency

Abstract

As somatic cells are converted into induced pluripotent stem cells (iPSCs), their chromatin is remodeled to a pluripotent configuration with unique euchromatin-to-heterochromatin ratios, DNA methylation patterns, and enhancer and promoter status. The molecular machinery underlying this process is largely unknown. Here, we show that embryonic stem cell (ESC)-specific factors Dppa2 and Dppa4 play a key role in resetting the epigenome to a pluripotent state. They are induced in reprogramming intermediates, function as a heterodimer, and are required for efficient reprogramming of mouse and human cells. When co-expressed with Oct4, Klf4, Sox2, and Myc (OKSM) factors, Dppa2/4 yield reprogramming efficiencies that exceed 80% and accelerate reprogramming kinetics, generating iPSCs in 2 to 4 days. When bound to chromatin, Dppa2/4 initiate global chromatin decompaction via the DNA damage response pathway and contribute to downregulation of somatic genes and activation of ESC enhancers, all of which enables an efficient transition to pluripotency. Our work provides critical insights into how the epigenome is remodeled during acquisition of pluripotency.

A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation

“…5B-C). Importantly, Dppa2 and Smarca5 proteins have been shown to physically interact in ESCs (Hernandez et al 2018), suggesting they may function together to regulate their ZGA target genes. Consistent with our overexpression results, analysis of recently published Smarca5 KO transcriptome data (Barisic et al 2019) revealed that loss of Smarca5 led to downregulation of ZGA transcripts ( Fig.…”

“…Finally, given their co-localization in two-cell embryos ( Fig. 5B-C), physical interaction in ESCs (Hernandez et al 2018) and similar transcriptional effects ( Fig. 4B-D, S5D), we sought to understand the mechanistic interdependencies, if any, between Dppa2 and Smarca5 through a series of KO and overexpression experiments analysed by quantitative reverse transcription PCR.…”

Dppa2/4 target chromatin bivalency enabling multi-lineage commitment

“…Bivalent chromatin is a signature of developmental gene promoters in pluripotent cells, however, it is unclear how it is targeted. We, and others, have recently revealed binding of Dppa2/4 at gene promoters in mouse ESCs ( 6, 7, 9–11 ) (Fig. 1E).…”

“…(E) Genome browser screenshot showing Dppa2 (blue), Dppa4 (purple) binding and H3K4me3 (green) and H3K27me3 (red) histone modifications across a 394kb region of chromosome 1. Input, Dppa2 and Dppa4 data reanalysed from ( 9 ), H3K4me3 and H3K27me3 data from this study. H3K4me3 promoters highlighted in green, bivalent promoters highlighted in yellow, inactive promoters highlighted in red.…”

“…Recently, we and others revealed a role for the small heterodimerising nuclear proteins Developmental Pluripotency Associated 2 (Dppa2) and 4 (Dppa4), in regulating zygotic genome activation (ZGA)-associated transcripts ( 6–8 ). Excitingly, Dppa2/4 also bind non-ZGA gene promoters, including bivalent promoters ( 6, 9–11 ), however the significance of this is unknown. Intriguingly, single and double zygotic knockout mice survive early embryogenesis only to succumb to lung and skeletal defects shortly after birth, despite these proteins not being expressed in these, or any other adult somatic tissue, uncoupling when they are present from their developmental phenotype ( 12, 13 ).…”