Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [scRNA-seq]

Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation. Whole chicken embryo eyes were collected for snRNA-seq via the split-pool barcoding method, using the Parse Biosciences Single Cell Whole Transcriptome Kit Chemistry Version 1 (Parse Biosciences, SB2001). An eye from each of 3 chickens were pooled per condition, across the following conditions: embryonic day 4, embryonic day 5, embryonic day 4 6 hours post-retinectomy, and embryonic day 4 6 hours post-retinectomy and FGF2 treatment. All nuclei were processed in aggregate across 7 sublibraries. Sublibraries 1-3 were sequenced across 3 distinct sequencing lanes.