Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [CUT&RUN]

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. Cleavage Under Targets and Release Using Nuclease sequencing (CUT&RUN-seq) was performed according to manufacturer protocol, with slight modification, as described. Chicken embryos were obtained from Michigan State University and lenses were dissected from embryonic day 4.5 chicken embryos. Dissected lenses were collected on ice and pooled into 3 biological replicates consisting of approximately 44 lenses each. Histone modifications and PRC2 complex members were assayed, as described.