The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [evolutionary study]

Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. We show that deletion or ectopic expression of Grh causes loss or gain of DNA accessibility, respectively. However, while Grh binding is necessary for enhancer accessibility, it is insufficient to activate enhancers. Finally, we show that human Grh homologs, GRHL1/2/3, function similarly. We conclude that Grh binding is necessary and sufficient for the opening of epithelial enhancers, but not for their activation. Our data support the model that complex spatiotemporal expression patterns are controlled by regulatory hierarchies in which pioneer factors, such as Grh, establish tissue-specific accessible chromatin landscapes upon which other factors can act. ATAC-seq on 11 Drosophila Species to identify co-motifs in conserved Grainyhead enhancers.

转录增强子（transcriptional enhancers）可作为多种转录因子的结合平台，以调控基因表达。目前，增强子序列如何在活体内决定核小体占据、转录因子招募以及转录激活，仍未明确。本研究通过对一组果蝇（Drosophila）近交品系开展转座酶可及性测序（ATAC-seq），发现影响Grainyhead（Grh）结合位点的单核苷酸多态性（SNPs）可直接决定上皮增强子的染色质可及性。我们证实，敲除Grh或异位表达Grh，分别会导致DNA可及性丧失或增强。不过，尽管Grh结合对于增强子可及性是必需的，但仅靠其结合不足以激活增强子。最后，我们发现人类的Grh同源基因GRHL1/2/3也具有相似的功能。综上，我们认为Grh结合对于上皮增强子的染色质开放是必需且充分的，但并非增强子激活所必需。本研究数据支持如下调控层级模型：复杂的时空表达模式由调控层级所控制，其中先锋因子（pioneer factors）如Grh可建立组织特异性的可及染色质景观，其他转录因子可在此基础上发挥功能。本研究还对11种果蝇开展了ATAC-seq，以鉴定保守Grainyhead增强子中的共基序。