The genetic architecture of cell type-specific cis regulation in maize

• 成果类型: Article
• 署名作者: Marand, Alexandre P.; Jiang, Luguang; Gomez-Cano, Fabio; Minow, Mark A. A.; Zhang, Xuan; Mendieta, John P.; Luo, Ziliang; Bang, Sohyun; Yan, Haidong; Meyer, Cullan; Schlegel, Luca; Johannes, Frank; Schmitz, Robert J.
• 署名单位: University System of Georgia; University of Georgia; University of Michigan System; University of Michigan; University System of Georgia; University of Georgia; Technical University of Munich
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8483
• DOI: 10.1126/science.ads6601
• 发表日期: 2025-04-18
• 关键词: transcription factors; homeobox gene; arabidopsis; adaptation; format; FAMILY; identification; association; TRANSITION; SEQUENCES

摘要

Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of more than 0.7 million nuclei across 172 Zea mays (maize) inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and revealed how historical transposon activity has shaped the cis-regulatory landscape. Leveraging population genetics principles, we fine-mapped about 22,000 chromatin accessibility-associated genetic variants with widespread cell type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR-binding sites were the most prevalent determinants of chromatin accessibility. Finally, integrating chromatin accessibility-associated variants, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular contexts to alter maize flowering.