Fig. 7: A single-cell rice atlas combines multi-species data to uncover the evolution of CREs.

a, Overview of the nine organs analysed using scATAC-seq, the seedling organs examined via snRNA-seq and the crown root studied through Slide-seq in rice. b, A QTN was identified within an endosperm-specific ACR approximately 1 kb upstream of the OsGluA2 gene, which is associated with increased seed protein content. TCP4 exhibited reduced motif accessibility during xylem development in O. sativa, while TCP4 displayed increased accessibility along the RDX trajectory in Z. mays, paralleling scRNA-seq expression patterns during RDX development. c, Despite being within facultative heterochromatin, H3K27me3-broad ACRs are accessible in many cell types, providing a physical entry point for PRC2 to bind. Several lines of evidence support that the H3K27me3-broad ACRs contain silencer CREs. Specifically, these ACRs are linked to transcriptionally silent genes, enriched for PRE motifs, enriched for TF family motifs (AP2 and C2H2) reported to recruit PRC2, and enriched for PRC2 subunit (EMF2b) ChIP-seq peaks. d, The analysis of leaf cell types across these species revealed an enrichment of cell-type-specific ACRs in species-specific regions. These species-specific ACRs were enriched within L1-derived cells compared to all others examined. e, We found an enrichment of CNS in cell-type-specific ACRs. Although some CNS ACRs retained the same cell-type specificity between O. sativa and Z. mays, these CNS ACRs often switched tissue or cell-type accessibility between grass species. AL, aleurone. f, A database, RiceSCBase, was developed to provide access to the rice atlas data, featuring tools for marker visualization, TF motif enrichment and trajectory analysis.