Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence

Xiaoyu Tu, Sibo Ren, Wei Shen, Jianjian Li, Yuxiang Li, Chuanshun Li, Yangmeihui Li, Zhanxiang Zong, Weibo Xie, Donald Grierson, Zhangjun Fei, Jim Giovannoni, Pinghua Li () and Silin Zhong ()
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Xiaoyu Tu: Chinese Academy of Sciences
Sibo Ren: The Chinese University of Hong Kong
Wei Shen: The Chinese University of Hong Kong
Jianjian Li: The Chinese University of Hong Kong
Yuxiang Li: The Chinese University of Hong Kong
Chuanshun Li: Shanghai Jiao Tong University
Yangmeihui Li: Shanghai Jiao Tong University
Zhanxiang Zong: Huazhong Agricultural University
Weibo Xie: Huazhong Agricultural University
Donald Grierson: Zhejiang University
Zhangjun Fei: Cornell University
Jim Giovannoni: Cornell University
Pinghua Li: Shandong Agricultural University
Silin Zhong: Chinese Academy of Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract Non-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. However, cistrome dynamics in plants remain largely underexplored. Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. Although the function of GLKs is conserved, most of their binding sites are species-specific. Conserved binding sites are often found near photosynthetic genes dependent on GLK for expression, but sites near non-differentially expressed genes in the glk mutant are nevertheless under purifying selection. The binding sites’ regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. Our study show that genome cis-variation caused wide-spread TF binding divergence, and most of the TF binding sites are genetically redundant. This poses a major challenge for interpreting the effect of individual sites and highlights the importance of quantitatively measuring TF occupancy.

Date: 2022
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DOI: 10.1038/s41467-022-35438-4

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