Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
PLoS One. 2011 Apr 5;6(4):e14778. doi: 10.1371/journal.pone.0014778.
Hox genes encode a family of transcription factors that are key developmental regulators with a highly conserved role in specifying segmental diversity along the metazoan body axis. Although they have been shown to regulate a wide variety of downstream processes, direct transcriptional targets have been difficult to identify and this has been a major obstacle to our understanding of Hox gene function. We report the identification of genome-wide binding sites for the Hox protein Ultrabithorax (Ubx) using a YFP-tagged Drosophila protein-trap line together with chromatin immunoprecipitation and microarray analysis. We identify 1,147 genes bound by Ubx at high confidence in chromatin from the haltere imaginal disc, a prominent site of Ubx function where it specifies haltere versus wing development. The functional relevance of these genes is supported by their overlap with genes differentially expressed between wing and haltere imaginal discs. The Ubx-bound gene set is highly enriched in genes involved in developmental processes and contains both high-level regulators as well as genes involved in more basic cellular functions. Several signalling pathways are highly enriched in the Ubx target gene set and our analysis supports the view that Hox genes regulate many levels of developmental pathways and have targets distributed throughout the gene network. We also performed genome-wide analysis of the binding sites for the Hox cofactor Homothorax (Hth), revealing a striking similarity with the Ubx binding profile. We suggest that these binding profiles may be strongly influenced by chromatin accessibility and provide evidence of a link between Ubx/Hth binding and chromatin state at genes regulated by Polycomb silencing. Overall, we define a set of direct Ubx targets in the haltere imaginal disc and suggest that chromatin accessibility has important implications for Hox target selection and for transcription factor binding in general.
Hox 基因编码一类转录因子，它们在动物体轴的节段多样性中具有高度保守的作用，是关键的发育调控因子。尽管已经证明它们可以调节广泛的下游过程，但直接的转录靶标很难确定，这一直是我们理解 Hox 基因功能的主要障碍。我们使用 YFP 标记的果蝇蛋白陷阱系，结合染色质免疫沉淀和微阵列分析，报告了 Hox 蛋白 Ultrabithorax (Ubx) 在平衡棒 imaginal 盘基因组范围内的结合位点的鉴定。我们在平衡棒 imaginal 盘高置信度地鉴定了 Ubx 结合的 1147 个基因，平衡棒 imaginal 盘是 Ubx 功能的一个突出部位，它指定平衡棒而不是翅膀发育。这些基因的功能相关性得到了它们与翅膀和平衡棒 imaginal 盘之间差异表达基因重叠的支持。Ubx 结合基因集高度富集于参与发育过程的基因，其中包括高级别调控因子以及参与更基本细胞功能的基因。几个信号通路在 Ubx 靶基因集中高度富集，我们的分析支持 Hox 基因调节许多发育途径的水平，并具有分布在整个基因网络中的靶标。我们还对 Hox 共因子 Homothorax (Hth) 的结合位点进行了全基因组分析，揭示了与 Ubx 结合谱的惊人相似性。我们认为这些结合谱可能受到染色质可及性的强烈影响，并为 Ubx/Hth 结合与 Polycomb 沉默调控基因的染色质状态之间的联系提供了证据。总的来说，我们在平衡棒 imaginal 盘中定义了一组直接的 Ubx 靶标，并表明染色质可及性对 Hox 靶标选择和一般转录因子结合具有重要意义。
