Chd4 remodels chromatin to control retinal cell type specification and lineage termination

Abstract

During development, neural progenitor cells modify their output over time to produce different types of neurons and glia in chronological sequences. Previous studies have shown that epigenetic processes play a crucial role in regulating neural progenitor potential, but the underlying mechanisms are not well understood. Here, we hypothesized that nucleosome remodelling would regulate the competence transitions of retinal progenitors. We generated retina-specific conditional knockouts (cKOs) in the key nucleosome remodelling enzyme Chd4. Chd4 cKOs overproduced early-born retinal ganglion and amacrine cells. Postnatally, later-born rod photoreceptors were drastically underproduced. Concomitantly, progenitors failed to be exhausted at late phases of development and ultimately overproduced Muller glia. To determine how Chd4 regulates the genome, we used cut&run-seq to reveal Chd4 genome occupancy, and ATAC-seq experiments to visualize nucleosome remodelling. These data revealed that genome accessibility was significantly increased at [~]10,000 regulatory elements and [~]4,000 genes in the Chd4 cKO. Together, these results suggest that Chd4 restricts the genome to repress progenitor identity and promote rod photoreceptor production. Accordingly, multiplexed single-cell transcriptomics demonstrated that deletion of Chd4 led to markedly divergent gene expression profiles. However, despite overproduction of early fates and underproduction of later-born rods, the perinatal transition between early and late progenitor competence was not altered as determined by birthdating experiments and transcriptomic signatures. Taken together, our data suggest that Chd4-dependent chromatin remodelling regulates cell fate specification, and is also required to terminate retinal neurogenesis, but that it does not regulate the progenitor competence windows that restrict early- vs. late-cell-type production. Key findings1) Chd4 cKOs exhibit a strong shift in neurogenesis, with early-born neurons overproduced and late-born neurons underproduced. 2) We present an epigenetic atlas that combines the occupancy of NuRD proteins such as Chd4 and Mbd3, with nucleosome remodelling data and transcriptomic correlates. 3) We show that NuRD regulates the competence transition that terminates the retinal lineage but not earlier competence transitions, showing for the first time that the epigenetic mechanisms governing retinal competence transitions may vary.