Nevil Markus, Bondra Eliana R, Schulz Katharine N, Kaplan Tommy, Harrison Melissa M
Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706.
School of Computer Science and Engineering, The Hebrew University of Jerusalem, 91904, Israel.
Genetics. 2017 Feb;205(2):605-620. doi: 10.1534/genetics.116.195685. Epub 2016 Dec 22.
It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.
有人提出转录因子结合具有时间动态性，且结合的变化决定转录输出。然而，该模型基于相对较少的在多个发育阶段检测转录因子结合的例子。关键转录因子颗粒头（Grh）从真菌到人类都保守存在，并控制众多组织中的上皮发育和屏障形成。拥有单个颗粒头（grh）基因的黑腹果蝇提供了一个研究这个保守因子的绝佳系统。为了确定时间上不同的结合事件是否允许Grh在不同组织类型中控制细胞命运特化，我们结合使用染色质免疫沉淀测序（ChIP-seq）和RNA测序（RNA-seq）来阐明在胚胎发育的四个阶段（跨越5-17期）和幼虫组织中由Grh控制的基因调控网络。与预期相反，我们发现Grh在数天的发育过程中一直与至少1146个基因组位点结合。与这种稳定的DNA占据情况相反，其表达受Grh调控的基因子集有所不同。Grh从在发育早期主要作为转录抑制因子发挥作用转变为在后期主要作为激活因子发挥作用。我们的数据表明，Grh在依赖Grh的转录程序开始之前就与靶基因结合，这表明它为后续招募执行阶段特异性Grh功能的其他因子奠定了基础。
