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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #409456

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: DAP-seq hints at potential binding sites of transcription factors for functional studies

item FAHEY, AUDREY - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item RUGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/28/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Sorghum bicolor is a valuable crop for food, fodder, and forage. Despite being a crop durable to heat and drought, abiotic stress still negatively impacts root and shoot development which can result in poor yields. Previous studies in Arabidopsis have identified three transcription factors (TFs) as important for root and shoot system architecture: SCL23, SCL3, and SHR; however, their function and binding behaviors have been understudied in sorghum. Here, we use DNA affinity purification sequencing, or DAP-seq, to inform hypotheses toward the binding behaviors and functional roles these TFs play in sorghum root architectures. This in vitromethod identifies all potential TF-DNA binding regions without cell-specific contexts. While this output generates many spurious binding regions, DAP-seq does increase the likelihood of identifying novel, functionally important binding regions across different tissues. TF binding peaks were therefore filtered for proximity to promoter regions of gene models. From there, we confirmed previously reported orthologs of gene regulatory targets and identified novel regions and motifs for further study. The genes corresponding to the binding motifs were then correlated to gene ontology (GO) terms and integrated with data from epigenetic and RNA-seq profiles to construct gene regulatory networks. This provides insight for potential targets that can be explored through functional characterization of EMS-induced SNP populations to determine their roles in root growth, development, and abiotic stress response. This project was funded by the USDA-ARS award number 8062-21000-044-000D.