Department of Systems Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, Albert Sherman Center, Worcester, MA 01605, USA.
G3 (Bethesda). 2023 Jul 5;13(7). doi: 10.1093/g3journal/jkad096.
Chromatin modifiers and transcriptional cofactors (collectively referred to as CFs) work with DNA-binding transcription factors (TFs) to regulate gene expression. In multicellular eukaryotes, distinct tissues each execute their own gene expression program for accurate differentiation and subsequent functionality. While the function of TFs in differential gene expression has been studied in detail in many systems, the contribution of CFs has remained less explored. Here, we uncovered the contributions of CFs to gene regulation in the Caenorhabditis elegans intestine. We first annotated 366 CFs encoded by the C. elegans genome and assembled a library of 335 RNAi clones. Using this library, we analyzed the effects of individually depleting these CFs on the expression of 19 fluorescent transcriptional reporters in the intestine and identified 216 regulatory interactions. We found that different CFs regulate different promoters, and that both essential and intestinally expressed CFs have the greatest effects on promoter activity. We did not find all members of CF complexes acting on the same set of reporters but instead found diversity in the promoter targets of each complex component. Finally, we found that previously identified activation mechanisms for the acdh-1 promoter use different CFs and TFs. Overall, we demonstrate that CFs function specifically rather than ubiquitously at intestinal promoters and provide an RNAi resource for reverse genetic screens.
染色质修饰因子和转录共激活因子（统称为 CFs）与 DNA 结合转录因子（TFs）一起工作，以调节基因表达。在多细胞真核生物中，不同的组织各自执行其特有的基因表达程序，以实现准确的分化和随后的功能。虽然在许多系统中已经详细研究了 TFs 在差异基因表达中的功能，但 CFs 的贡献仍然较少被探索。在这里，我们揭示了 CFs 对秀丽隐杆线虫肠道基因调控的贡献。我们首先注释了由秀丽隐杆线虫基因组编码的 366 个 CFs，并构建了一个包含 335 个 RNAi 克隆的文库。利用这个文库，我们分析了单独耗尽这些 CFs 对肠道中 19 个荧光转录报告基因表达的影响，并鉴定了 216 个调控相互作用。我们发现，不同的 CFs 调节不同的启动子，并且必需的和肠道表达的 CFs 对启动子活性的影响最大。我们没有发现 CF 复合物的所有成员都作用于同一组报告基因，而是发现每个复合物成分的启动子靶标存在多样性。最后，我们发现，先前鉴定的 acdh-1 启动子的激活机制使用不同的 CFs 和 TFs。总体而言，我们证明 CFs 在肠道启动子上特异性地发挥作用，而不是普遍地发挥作用，并提供了一个用于反向遗传筛选的 RNAi 资源。
