Fig. 2

Genome-wide regulatory map and experimental validations. A Basenji2-long model prediction performance evaluated by Pearson correlation coefficient (PCC) across four plant species, using different DNA input lengths to select the optimal length based on independent test sets (N denotes its sample size). B Distance distribution of candidate CREs from the TSS of its target genes identified by the Basenji2-long model of maize. C Overlap proportions and enrichment fold of candidate CREs across five genomic components. D Reappearance rates of candidate CREs in three experimental datasets, comparing CRE-gene pairs with experimentally identified CREs (top), and tissue-specific candidate CREs identified by the omics-modified gradient × input contribution score (see the “Methods” section) (bottom panel). E Overlap analysis of candidate CREs with four types of QTLs. Red bars: number of overlapping CREs, green bars: proportion of QTLs overlapping with CREs. F Selection, synthesis, and UMI-STARR-seq screening of candidate CRE sequences in maize protoplasts. G Distribution of 21,152 CREs after sequencing, showing total sequences (forward and reverse orientations) in each group, corresponding to Fig. 2F. H CRE activities of synthesized candidate CRE sequences. A volcano plot of log2FC scores (i.e., CRE activity) against –log10-transformed BH adjusted P-value from DESeq2 is shown. The CRE activity of a candidate CRE sequence (ID:7424) of Zm00001d005208 is highlighted. I Number and percentage of 8650 enhancers in five groups. J A representative enhancer validated for Zm00001d005208. The first panel shows the genomic positions of Zm00001d005208 and the enhancer (seq ID: 7424). The second panel displays the gradient × input contribution score from the Basenji2-long model, highlighting 14 candidate CREs (marked in orange at the peak summits). Subsequent panels show genomic tracks of chromatin interactions, RNA-seq, ATAC-seq, H3K27ac, and eQTLs for the region, with eQTL (chr2.s_163640429) within the candidate enhancer highlighted