The native cistrome and sequence motif families of the maize ear

• DOI: 10.1371/journal.pgen.1009689
• Publication Date: 2021-08-12T19:07:05Z
• Authors: Savannah D. Savadel; Thomas Hartwig; Zachary M. Turpin; Daniel L. Vera; Pei-Yau Lung; Xin Sui; Max Blank; Wolf B. Frommer; Jonathan H. Dennis; Jinfeng Zhang; Hank W. Bass
• Keywords: Chromatin immunoprecipitation; DNA binding site; Sequence motif

Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define complete set of transcription factor (TF) binding sites. Although TF-binding sites are known be generally located within accessible chromatin regions (ACRs), pinpointing these DNA elements globally remains challenging. Current approaches primarily identify for a single TF (e.g. ChIP-seq), or detect ACRs but lack resolution consistently DNAse-seq, ATAC-seq). To address this challenge, we developed M Nase-defined cistrome- O ccupancy A nalysis (MOA-seq), high-resolution (< 30 bp), high-throughput, genome-wide strategy putative ACRs. We used MOA-seq on developing maize ears as proof concept, able cistrome 145,000 MOA footprints (MFs). While substantial majority (76%) ATAC-seq intersected with MFs, only minority MFs overlapped ATAC peaks, indicating were novel not detected by ATAC-seq. associated promoters significantly enriched long-range interaction sites, including well-characterized FASCIATED EAR4, KNOTTED1, TEOSINTE BRANCHED1. Importantly, improved spatial prediction allowed us 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied across genome. Our study presents simple, efficient, approach motifs genome-wide, ultimately native atlas.