MOA-seq footprints improve the spatial resolution of TF binding event prediction.

(A-F) ChIP-seq binding peaks of (A-B) FEA4 or (E-F) TB1, ATAC-Seq coverage (Ac) and peaks (Ap), MOA-seq footprint coverage (Mfc) and peaks (Mfp), and MOA-seq motif om015 in the promoter region of example genes (A) zw18-like (GRMZM2G039505), (B) bx9 (GRMZM2G161335), (E) nactf49 (GRMZM2G347043), and (F) d8 (GRMZM2G144744). (C, G) MOA-seq motif (C) om015 (G) dym33, aligned to their best database hit (footprintdb) of bzip and TCP family, respectively. The asterisk for (G) dym33 indicates that only a portion of the larger dym33 logo is shown. (D, H) Enrichment of motifs (D) om015 and a control motif om006 within FEA4 ChIP-seq peaks, or (H) dym33 and control motif dym36 with TB1 ChIP-seq peaks, relative to the mappable B73 genome (gen.), and the 3 kb, non-ORF overlapping, region upstream of B73 gene models (prom.). (I) Genome-wide overlap analysis of base pairs shared between MOA (MOA, MFs) and ChIP-seq of 104 TFs [27] or the MNase control (CTRL). (J) Representative example of the complex landscape of TF and MFs profiles surrounding tip1 (Zm00001eb00373). TF tracks shown: MYB, TF55 rep1 GSM4095564; C2C2 TF235 rep2 GSM4095532,; bHLH, TF6 rep2 GSM4095589; TCP, TF237 rep1 GSM4095534.