Hu Yanhui, Rodiger Jonathan, Liu Yifang, Gao Chenxi, Liu Ying, Qadiri Mujeeb, Veal Austin, Bulyk Martha L, Perrimon Norbert
Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
Drosophila RNAi Screening Center, Harvard Medical School, Harvard University, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
Genetics. 2025 May 2. doi: 10.1093/genetics/iyaf082.
Sequence-specific transcription factors (TFs) are key regulators of many biological processes, controlling the expression of their target genes through binding to the cis- regulatory regions such as promoters and enhancers. Each TF has unique DNA binding site motifs, and large-scale experiments have been conducted to characterize TF-DNA binding preferences. However, no comprehensive resource currently integrates these datasets for Drosophila. To address this need, we developed TF2TG ("transcription factor" to "target gene"), a comprehensive resource that combines both in vitro and in vivo datasets to link transcription factors (TFs) to their target genes based on TF-DNA binding preferences along with the protein-protein interaction data, tissue-specific transcriptomic data, and chromatin accessibility data. Although the genome offers numerous potential binding sites for each TF, only a subset is actually bound in vivo, and of these, only a fraction is functionally relevant. For instance, some TFs bind to their specific sites due to synergistic interactions with other factors nearby. This integration provides users with a comprehensive list of potential candidates as well as aids users in ranking candidate genes and determining condition-specific TF binding for studying transcriptional regulation in Drosophila.
序列特异性转录因子（TFs）是许多生物过程的关键调节因子，它们通过与启动子和增强子等顺式调节区域结合来控制其靶基因的表达。每个转录因子都有独特的DNA结合位点基序，并且已经进行了大规模实验来表征转录因子与DNA的结合偏好。然而，目前没有综合资源整合果蝇的这些数据集。为了满足这一需求，我们开发了TF2TG（“转录因子”到“靶基因”），这是一个综合资源，它结合了体外和体内数据集，基于转录因子与DNA的结合偏好以及蛋白质-蛋白质相互作用数据、组织特异性转录组数据和染色质可及性数据，将转录因子（TFs）与其靶基因联系起来。尽管基因组为每个转录因子提供了众多潜在的结合位点，但实际上只有一部分在体内被结合，而在这些结合位点中，只有一小部分具有功能相关性。例如，一些转录因子由于与附近其他因子的协同相互作用而与其特定位点结合。这种整合为用户提供了潜在候选基因的综合列表，同时帮助用户对候选基因进行排名，并确定特定条件下的转录因子结合，以研究果蝇中的转录调控。
