Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.
Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.
复制标题
GLK 转录因子结合的跨物种比较中有限的保守性表明存在广泛的顺反体分歧
DOI：
10.1038/s41467-022-35438-4
复制
发表时间：
2022-12-09
影响因子：
16.6
通讯作者：
Zhong, Silin
中科院分区：
文献类型：
--
作者：
Tu, Xiaoyu;Ren, Sibo;Shen, Wei;Li, Jianjian;Li, Yuxiang;Li, Chuanshun;Li, Yangmeihui;Zong, Zhanxiang;Xie, Weibo;Grierson, Donald;Fei, Zhangjun;Giovannoni, Jim;Li, Pinghua;Zhong, Silin
动物基因组中的非编码顺式调控变体是转录调控和表型多样性进化的重要驱动力。然而，植物中的顺式异构体动力学在很大程度上仍然未被探索。在这里，我们比较了GOLDEN 2-LIKE（GLK）转录因子在番茄、烟草、拟南芥、玉米和水稻中的结合。虽然GLK的功能是保守的，但它们的大多数结合位点是物种特异性的。保守的结合位点往往被发现附近的光合作用基因依赖于GLK的表达，但在GLK突变体的非差异表达的基因附近的网站，然而，纯化选择。结合位点的调控潜力可以通过机器学习模型使用定量基因组特征和TF共结合信息来预测。我们的研究表明，基因组顺式变异导致广泛的TF结合的分歧，和大多数TF结合位点是遗传冗余。这对解释单个站点的影响提出了重大挑战，并强调了定量测量TF占用的重要性。与微生物和哺乳动物不同，植物中的顺反子动力学尚不清楚。本文以GOLDEN 2-LIKE（GLK）转录因子为例，通过种间转化实验发现GLK结合位点大多数具有种特异性，结合差异是由顺式变异引起的。
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. Unlike microbes and mammals, cistrome dynamics in plants remains unclear. Here, using GOLDEN2-LIKE (GLK) transcription factor as an example, the authors find that most GLK binding sites are species-specific and the binding divergence is caused by cis-variations through inter-species transformation experiment.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btac525
发表时间：
2022-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
通讯作者：
--
影响因子：
4.5
作者：
Cusanovich DA;Pavlovic B;Pritchard JK;Gilad Y
通讯作者：
Gilad Y
影响因子：
2.9
作者：
Jenkins, MT
通讯作者：
Jenkins, MT
DOI：
10.1126/science.1183621
发表时间：
2010-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Kasowski M;Grubert F;Heffelfinger C;Hariharan M;Asabere A;Waszak SM;Habegger L;Rozowsky J;Shi M;Urban AE;Hong MY;Karczewski KJ;Huber W;Weissman SM;Gerstein MB;Korbel JO;Snyder M
通讯作者：
Snyder M
影响因子：
7.2
作者：
Fitter, DW;Martin, DJ;Langdale, JA
通讯作者：
Langdale, JA