Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development

First author: Leonardo Jo; Affiliations: University of California, Davis (加利福尼亚大学戴维斯分校): CA, USA

Corresponding author: John J. Harada

The LEAFY COTYLEDON1 (LEC1) transcription factor is a central regulator of seed development, because it controls diverse biological programs during seed development, such as embryo morphogenesis, photosynthesis, and seed maturation. To understand how LEC1 regulates different gene sets during development, we explored the possibility that LEC1 acts in combination with other transcription factors. We identified and compared genes that are directly transcriptionally regulated by ABA-RESPONSIVE ELEMENT BINDING PROTEIN3 (AREB3), BASIC LEUCINE ZIPPER67 (bZIP67), and ABA INSENSITIVE3 (ABI3) with those regulated by LEC1. We showed that LEC1 operates with specific sets of transcription factors to regulate different gene sets and, therefore, distinct developmental processes. Thus, LEC1 controls diverse processes through its combinatorial interactions with other transcription factors. DNA binding sites for the transcription factors are closely clustered in genomic regions upstream of target genes, defining cis-regulatory modules that are enriched for DNA sequence motifs that resemble sequences known to be bound by these transcription factors. Moreover, cis-regulatory modules for genes regulated by distinct transcription factor combinations are enriched for different sets of DNA motifs. Expression assays with embryo cells indicate that the enriched DNA motifs are functional cis elements that regulate transcription. Together, the results suggest that combinatorial interactions between LEC1 and other transcription factors are mediated by cis-regulatory modules containing clustered cis elements and by physical interactions that are documented to occur between the transcription factors.

LEC1转录因子是植物种子发育的核心调控因子，其控制着种子发育过程中多个不同的生物学进程，包括胚胎形态发生、光合作用以及种子成熟。为了理解LEC1如何在发育过程中调控不同的基因集，作者探索了LEC1与其它转录因子组合发挥功能的可能。作者鉴定了能够直接受到AREB3、bZIP67以及ABI3转录调控的基因，并将其与LEC1靶向的基因进行比较。作者发现LEC1会与特定的转录因子互作来调控不同的基因集，从而影响不同的发育进程。因此，LEC1通过与不同转录因子的组合互作来控制不同的生物进程。转录因子的DNA结合位点会在靶基因上游的基因组区域聚集，也叫做顺式调控模块，这些模块中会富集一些与转录因子结合序列非常相似的DNA序列基序。此外，能够被不同转录因子靶向的基因的顺式调控模块会富集多个不同的DNA基序。胚胎细胞的表达试验显示富集的DNA基序是功能性的顺式元件，能够调控基因的转录。综上，本文的研究说明了LEC1与其它转录因子的组合互作是由包含聚集的顺式元件的顺式调控模块所介导的，亦或是由已知的两个转录因子之间的物理互作。

通讯：John J. Harada (https://biology.ucdavis.edu/people/john-harada)

个人简介：1975年，加利福尼亚大学洛杉矶分校，学士； 1981年，华盛顿大学，博士。

研究方向：植物胚胎发生和种子发育。

doi: https://doi.org/10.1073/pnas.1918441117

Journal: PNAS

First Published: December 31, 2019