The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [evolutionary study]. 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. Overall design: 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停靠平台，进而调控基因表达。增强子序列如何决定体内核小体占位、转录因子招募与转录激活，目前仍不明确。本研究通过对一组果蝇近交品系（Drosophila inbred strains）开展转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq），发现影响Grainyhead（Grh）结合位点的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）可因果性地决定上皮增强子的染色质可及性。研究证实，敲除Grh或对其进行异位表达，会分别导致DNA可及性（DNA accessibility）丧失或增强。然而，尽管Grh结合对于增强子可及性是必需的，但并不足以激活增强子。最后，本研究发现人类Grh同源物GRHL1/2/3亦发挥相似功能。本研究得出结论：Grh结合对于开放上皮增强子而言是必需且充分的，但并非增强子激活所必需。本研究数据支持如下调控模型：复杂的时空表达模式由多层调控层级所控制，其中先驱因子（pioneer factors）如Grh，可构建组织特异性的可及染色质景观（chromatin landscapes），以供其他调控因子发挥功能。实验整体设计：对11种果蝇开展ATAC-seq，以鉴定保守型Grainyhead增强子中的共调控基序。