hlh-1 is a myogenic transcription factor required for body-wall muscle specification during embryogenesis in Caenorhabditis elegans. Despite its well-known role in muscle specification, comprehensive regulatory control upstream of hlh-1 remains poorly defined. Here, we first established a statistical reference for the spatiotemporal expression of hlh-1 at single-cell resolution up to the second last round of divisions for most of the cell lineages (from 4- to 350-cell stage) using 13 wild-type embryos. We next generated lineal expression of hlh-1 after RNA interference (RNAi) perturbation of 65 genes, which were selected based on their degree of conservation, mutant phenotypes, and known roles in development. We then compared the expression profiles between wild-type and RNAi embryos by clustering according to their lineal expression patterns using mean-shift and density-based clustering algorithms, which not only confirmed the roles of existing genes but also uncovered the potential functions of novel genes in muscle specification at multiple levels, including cellular, lineal, and embryonic levels. By combining the public data on protein-protein interactions, protein-DNA interactions, and genetic interactions with our RNAi data, we inferred regulatory pathways upstream of hlh-1 that function globally or locally. This work not only revealed diverse and multilevel regulatory mechanisms coordinating muscle differentiation during C. elegans embryogenesis but also laid a foundation for further characterizing the regulatory pathways controlling muscle specification at the cellular, lineal (local), or embryonic (global) level.

中文翻译：

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秀丽隐杆线虫胚胎发生过程中肌肉特异性转录因子hlh-1的多级调节。

hlh-1是秀丽隐杆线虫胚胎发生过程中体壁肌肉规格所需的成肌转录因子。尽管它在肌肉规范中起着众所周知的作用，但是在hlh-1上游的全面调节控制仍不清楚。在这里，我们首先使用13种野生型为大多数细胞谱系（从4到350细胞阶段）的单细胞分辨率直至第二轮分裂的hlh-1时空表达建立了统计参考。胚胎。接下来我们生成hlh-1的线性表达RNA干扰（RNAi）干扰了65个基因，这些基因是根据其保守程度，突变表型和在发育中的已知作用而选择的。然后，我们使用均值漂移和基于密度的聚类算法根据其线性表达模式进行聚类，从而比较了野生型和RNAi胚胎之间的表达谱，这不仅证实了现有基因的作用，还揭示了新基因的潜在功能在肌肉规格上有多个层次，包括细胞，系和胚胎水平。通过将有关蛋白质-蛋白质相互作用，蛋白质-DNA相互作用和遗传相互作用的公共数据与我们的RNAi数据相结合，我们推断了hlh-1上游的调控途径在全球或本地运作。这项工作不仅揭示了秀丽隐杆线虫胚胎发生过程中协调肌肉分化的多种多样的多级调控机制，而且为进一步表征在细胞，直系（局部）或胚胎（整体）水平上控制肌肉规格的调控途径奠定了基础。