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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 #417523
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Binding Site Preferences of Sorghum GRAS Transcription Factors Across Monocots

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

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/20/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The GRAS transcription factor (TF) family is a plant-specific TF family that is heavily involved in plant inflorescence development and root architecture. The effect of these TFs has been characterized more in Arabidopsis, and less so in Sorghum bicolor and other monocots. In order to address this, three representative sorghum GRAS TFs (SHORT ROOT, SCARECROW-LIKE 3, and SCARECROW-LIKE 23) were characterized using DNA affinity purification and sequencing (DAP-seq). To do this, each TF precipitated genomic DNA fragments from Sorghum bicolor, Zea mays, and Oryza sativa. The precipitated fragments were sequenced, then data processed to determine the TF binding sites in each background. This has generated the first-ever DAP-seq profile of these TFs in sorghum and produced data for cross-species comparison. Promoters with high GRAS TF binding hits were often associated with genes involved in amino acid processing, stress response, and potential root architecture development. Motif analysis of novel and unique DNA motifs showed a unique recognition motif signature for each TF. We identified putative GRAS-specific DNA binding motifs that were over-represented in promoter sequences of protein coding genes. Then, we confirmed them as real motifs through frequency evaluation across all promoter regions in sorghum, maize, and rice. They were unique compared to other well-known TF family recognition motifs like WRKY and NAC. We combined these GRAS binding profiles with epigenetic data to further curate potential regulatory non-coding target sequences that could be candidates for CRISPR editing for downstream functional characterization and agronomic trait generation. This project was funded by the USDA-ARS award number 8062-21000-044-000D.