Transient Partial Inhibition of DNA Polymerase α Promotes Chromatin Plasticity and Enhances Human Cell Reprogramming

Abstract

Somatic cell reprogramming requires extensive remodeling of epigenomic and transcriptional state, yet the mechanisms that enhance chromatin plasticity during cell-fate conversion remain incompletely understood. Beyond its essential role in genome duplication, DNA replication provides a dynamic window for chromatin remodeling and may therefore influence cellular plasticity during reprogramming. Here, we show that low-dose, transient inhibition of the lagging-strand DNA polymerase (Pol ) complex markedly enhances reprogramming of human peripheral blood mononuclear cells into induced pluripotent stem cells (iPSCs). Fine-tuned inhibition of the catalytic subunit PolA1 increases cell survival under reprogramming-associated stress and enhances cellular resilience to diverse external stresses, preserves genomic stability, and accelerates the acquisition of pluripotent features. PolA1-inhibited cells undergo rapid increases in chromatin accessibility following reprogramming factor delivery and display accelerated progression toward the iPSC state. Consistent with enhanced developmental plasticity, colonies derived from PolA1 inhibitor-treatment display dome-shaped morphology, increased expression of several naive pluripotency markers such as SUSD2. Integrated imaging and single-nucleus multiomic analyses establish transient PolA1 inhibition as a potent regulator of early chromatin remodeling during reprogramming. Functionally, PolA1 inhibitor-derived iPSC lines maintain stable pluripotency and exhibit enhanced differentiation potential, including increased embryoid body budding and accelerated cardiomyocyte differentiation and maturation. Notably, transient and low-dose PolA1 inhibition alters replication-coupled histone incorporation without reducing DNA replication speed or affecting cell cycle progression. This two-step regime primes human PBMCs for sustained gains in reprogramming efficiency with pre- and post-treatment. Together, these findings identify replication-coupled chromatin regulation as an underappreciated mechanism regulating human cell fate plasticity and demonstrate that transient modulation of Pol can simultaneously enhance epigenomic plasticity and preserve genome stability during reprogramming.