Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [Multiome snRNA/snATAC]
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.  Overall design: Embryonic day 4 (E4) and day 5 (E5) chicken eyes were profiled for combined single-nucleus RNAseq and ATACseq using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression library preparation workflow (10X Genomics, 1000285 & 1000230) following 10X Genomics protocol CG000338 Rev F. Eyes from 3 embryos were pooled per reaction.