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bioRxiv · 10.1101/2024.08.17.608383

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

Marand, A. P.·Jiang, L.·Gomez-Cano, F. A.·Minow, M. A. A.·Zhang, X.·Mendieta, J. P.·Luo, Z.·Bang, S.·Yan, H.·Meyer, C.·Schlegel, L.·Johannes, F.·Schmitz, R. J.
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Abstract

AbstractGene 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 >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 [~]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 context to alter maize flowering.

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Marand, A. P., Jiang, L., Gomez-Cano, F. A., Minow, M. A. A., Zhang, X., Mendieta, J. P., Luo, Z., Bang, S., Yan, H., Meyer, C., Schlegel, L., Johannes, F., Schmitz, R. J.. 2024-08-17. The genetic architecture of cell-type-specific cis-regulation. https://doi.org/10.1101/2024.08.17.608383

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