背景回顾：Non-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. 

提出问题：However, cistrome dynamics in plants remain largely underexplored. 

主要研究：Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. 

结果1-功能保守，结合位点变异：Although the function of GLKs is conserved, most of their binding sites are species-specific. 

结果2-保守结合位点：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. 

结果3-机器学习：The binding sites’ regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. 

结论：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.

Binding of the heterologously expressed ZmGLK1 in Arabidopsis genome.

动物基因组中的非编码顺式调控元件变异是驱动转录调控和表型多样性演化的重要因素。但是，植物中的顺反组（cistrome）动态在很大程度上还处于未开发的状态。本文中，作者比较了番茄、烟草、拟南芥、玉米和水稻中GLK转录因子的结合位点信息。尽管GLK的功能在不同植物间是保守的，但是其大部分结合位点具有物种特异性。保守的结合位点通常见于光合作用相关基因附近，这些光合基因依赖于GLK进行表达，但是glk突变体中非差异表达基因附近的GLK结合位点处于纯化选择中。利用量化基因组信息以及TF共结合信息进行机器学习模型训练，可以准确预测结合位点的调控潜能。本文的研究表明基因组顺式变异导致了广泛的转录因子结合分化，而大多数的转录因子结合位点在遗传上是冗余的。这些结果为诠释单个结合位点的影响带来重大的挑战，同时也突出了量化测定转录因子占据的重要性。

** 钟思林 **

doi: https://doi.org/10.1038/s41467-022-35438-4

Journal: Nature Communications

Published date: December 09, 2022