{"doi":"10.1371/journal.pgen.1009689","title":"The native cistrome and sequence motif families of the maize ear","abstract":"Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.","journal":"PLoS Genetics","year":2021,"id":155575,"datarank":1.3464536746083553,"base_score":4.07753744390572,"endowment":4.07753744390572,"self_citation_contribution":0.611630616585858,"citation_network_contribution":0.7348230580224971,"self_endowment_contribution":0.611630616585858,"citer_contribution":0.7348230580224971,"corpus_percentile":null,"corpus_rank":null,"citation_count":58,"citer_count":38,"citers_with_citation_signal":29,"citers_with_endowment":29,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9197,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.13012670.v1","10.6084/m9.figshare.13012673.v1"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":576218,"name":"Thomas Hartwig","orcid":"0000-0002-2707-2771","position":1,"is_corresponding":false},{"id":71872,"name":"Zachary M. Turpin","orcid":"0000-0002-6488-2503","position":2,"is_corresponding":false},{"id":218490,"name":"Daniel L. Vera","orcid":"0000-0003-2202-7397","position":3,"is_corresponding":false},{"id":175273,"name":"Pei-Yau Lung","orcid":null,"position":4,"is_corresponding":false},{"id":23478,"name":"Xin Sui","orcid":"0000-0001-5267-6115","position":5,"is_corresponding":false},{"id":658417,"name":"Max Blank","orcid":"0000-0002-5189-5049","position":6,"is_corresponding":false},{"id":658418,"name":"Wolf B. Frommer","orcid":"0000-0001-6465-0115","position":7,"is_corresponding":false},{"id":652953,"name":"Jonathan H. Dennis","orcid":"0000-0003-0621-7019","position":8,"is_corresponding":false},{"id":410098,"name":"Jinfeng Zhang","orcid":"0000-0002-7429-7615","position":9,"is_corresponding":false},{"id":71877,"name":"Hank W. Bass","orcid":"0000-0003-0522-0881","position":10,"is_corresponding":false},{"id":658416,"name":"Savannah D. Savadel","orcid":"0000-0002-0582-7766","position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-18T23:44:03.750995Z","pmid":"34383745","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}