William A. Ricci, Zefu Lu, Lexiang Ji, Alexandre P. Marand, Christina L. Ethridge et al.
Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Additionally, putative CREs display elevated transcriptional enhancer activities, as measured by STARR-seq. These results provide functional support for the widespread existence of CREs which act over large genomic distances to control gene expression.
William A. Ricci, Zefu Lu, Lexiang Ji, Alexandre P. Marand, Christina L. Ethridge, Nathalie G. Murphy, Jaclyn M. Noshay, Mary Galli, María Katherine Mejía-Guerra, Maria Colomé-Tatché, Frank Johannes, M. Jordan Rowley, Victor G. Corces, Jixian Zhai, Michael J. Scanlon, Edward S. Buckler, Andrea Gallavotti, Nathan M. Springer, Robert J. Schmitz, Xiaoyu Zhang. Widespread long-range cis-regulatory elements in the maize genome. 2019-11-18. https://doi.org/10.1038/s41477-019-0547-0
A leaf ATAC-seq library from B73 second leaves was cloned into an episomal STARR-seq reporter and transiently transfected into maize mesophyll protoplasts. The processed table summarizes the deposited RNA/input activity track for all fully covered leaf accessible chromatin regions (ACRs), including distal, proximal, and genic ACRs.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 11 files (ZIP)GSE120304_family.soft.gzGSE120304_STARR_B73_enhancer_activity_ratio.txt.gzGSE120304_STARR_column_header_descriptions.txt.gzREADME.txtreporting_summary.pdfSTARRseq_analysis_scripts/bidirectional_analysis/betabinomial.plSTARRseq_analysis_scripts/bidirectional_analysis/estimate_bidirectional_ACRs.RSTARRseq_analysis_scripts/read_mapping_pipeline/map_ATAC_Starr_seq_INPUT_example.shSTARRseq_analysis_scripts/regulatory_activity_analysis/estimate_regulatory_activity.Rsupplementary_information.pdfsupplementary_tables_1_4.xlsx