Fig. 2: The rice ACR atlas contextualized agronomically relevant ACRs and key TF motifs during cell progression.
From: A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution
a, The ratio of non-CDS QTNs overlapping with ACRs to all non-CDS QTNs. b, Percentage of non-CDS QTNs overlapping with ACRs. The significance test was done using one-tailed binomial test (alternative = ‘greater’; see ‘Construction of control sets for enrichment tests’ in the Methods). The error bars indicate the mean ± s.d. c, Analysis of cell-type-aggregate chromatin accessibility across 12 seed cell types and eight non-seed-related cell types, showing signatures of a QTN within an endosperm-specific ACR situated at the promoter region of OsGluA2. An endosperm-specific reduction of cytosine methylation was identified over the endosperm-specific ACR. mCG, mCHG and mCHH refer to DNA methylation at cytosines in the CG, CHG and CHH sequence contexts, respectively, where H denotes A, C or T. d, A total of 5,159 differentially methylated ACRs were identified, showing hypermethylation in early seedling tissue but hypomethylation within endosperm tissue. e, Enrichment of TF families based on their motifs within the 5,159 ACRs.The P value was computed using a one-tailed hypergeometric test (alternative = ‘greater’). bZIP, Basic Leucine Zipper; BBR/BPC, BARLEY B RECOMBINANT/BASIC PENTACYSTEINE; MADS, MCM1-AGAMOUS-DEFICIENS-SRF; EREBP, ETHYLENE-RESPONSIVE ELEMENT-BINDING PROTEIN. f, Deviations of motifs displaying enrichment in specific cell types (white frames) where their cognate TFs are known to be accumulated. MYB46, MYELOBLASTOSIS 46; PLT1, PLETHORA1; IDD4, INDETERMINATE DOMAIN 4. g, UMAP visualizations depict the cell progression of RDX in O. sativa. PM, procambial meristem; DX, developing xylem; Os, O. sativa. h, Relative chromatin accessibility of ACRs and TF genes associated with pseudotime (x axis). The left side displays three marker genes neighbouring the enriched ACRs along the trajectory gradient. OsWOX5, WUSCHEL-RELATED HOMEOBOX. i, Relative motif deviations for 351 TF motifs (left). Four motifs enriched along the trajectory gradient are shown on the right.
