(800-56) DAP-seq Supplements and Informs Functional Studies of Transcription Factors

Body of Abstract: Sorghum bicolor is a valuable crop for both food and biofuel industries. Impact in root and shoot architectures due to stressors can result in poor yields. Previous studies in Arabidopsis have identified three transcription factors (TFs) as potentially important for these architectures: SCL23, SCL3, and SHR; however, their function and binding behaviors have been understudied in sorghum. Here, we utilized DNA affinity purification sequencing, or DAP-seq, to gain insights into the functional role of these TFs. DAP-seq is a method where fragments of genomic DNA (gDNA) are bound by affinity-tagged TFs, and then sequenced. This in vitro method identifies all potential TF-DNA binding regions without cell-specific contexts. While there is a risk of identifying regions and motifs that do not correspond to particular annotated parts of the genome, this method increases the likelihood of identifying novel, functionally important binding regions. After sequencing and aligning the gDNA fragments, the TF-binding peaks were annotated for proximity to nearby gene models. From there, we confirmed previously reported and identified novel regions and motifs for further study. These peak data were used to determine the general TF binding pattern relative to the transcription start site. The genes corresponding to the binding motifs were then correlated to gene ontology (GO) terms, which hinted at possible future directions for functional studies. Before diving into experiments, integrating data from ChIP-seq, RNA-seq, and DAP-seq provided insight into more specific potential targets. Possible future directions include nutrient limitation experiments due to the TFs’ role in nutrient metabolic processes and studies in protein function due to their roles in protein folding and complex assembly. Impacts to these processes have possible implications in sorghum root and shoot architecture, potentially resulting in limited sorghum grain yield or reduced height. This project was funded by the USDA-ARS award number 8062-21000-044-000D.