Genome-binding/occupancy profiling of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells.
Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024.                                                                                                     PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA) and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent proteogenomic reprogramming to a functional blastomere-like state. Tankyrase-PARP1 inhibitor-regulated naïve stem cells (TIRN-SC) concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as two- to eight-cell (2C-8C) (e.g., TPRXL, HOX clusters, EOMES, DUXA, GATA6), pre-lineage morula (e.g., GATA4, SOX17, FOXA2), and naïve epiblast (e.g., LEFTY2, DNMT3L, NANOG) lineage-specifying pioneer factors; all in a hybrid, single-cell manner. Mapping of the single-cell transcriptome of TIRN-SC to human embryo references identified populations expressing hybrid transcriptional programs that not only spanned 2C-4C (pre-ZGA) and morula-ICM stages, but that were also augmented following brief induction of DUX4 expression (iDUX4).  Here, we performed ChIP-Seq profiling of PARP1, the core pluripotency factors NANOG, SOX2 and OCT4, phosphorylated-STAT3, BRD4 and modified histones H3K4me3, H3K27me3, H3K27ac. Co-binding analyses of core NANOG-SOX2-OCT4 (NSO) pluripotency factors with PARP1 (NSOP) identified genome-wide reprogramming of novel NSOP sites to DUX4-accessible distal and cis-regulatory enhancer regions in TIRN-SC. Gained NSOP enhancer regions possessed co-binding motifs for hundreds of the same 2C-8C-ICM-specific embryonic, and extraembryonic lineage-specifying pioneer factors (e.g., HOX, FOX, GATA, SOX, TBX families) that were concurrently co-expressed in TIRN-SC; suggesting that PARP1 and DUX4 chromatin co-binding cooperated with NSO core factors to regulate ZGA-associated lineage plasticity. Overall design: TIRN cells were originally reported as possessing a naive epiblast-like pluripotent stem cell molecular phenotype. We  used ChIP-Seq to examine the chromatin state  and the occupancy of PARP1, NANOG, SOX2 and OCT4 in TIRN stem cells. The hESC line RUES02 was cultured in parallel in primed (E8) or TIRN (LIF-3i) condition.