Differential gene expression across cell types underlies the development and cell physiology in multicellular organisms. C. elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates, however, to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNAPol DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit in order to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, sorted embryonic blastomeres and in different tissues from intact young adults by driving Dam fusion expression tissue-specifically. We obtained meaningful transcriptional footprints in line with RNA-seq studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 2362 candidate genes with putatively active transcription in XXX cells, among which the few known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.

中文翻译：

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在秀丽隐杆线虫中使用RNAPoI DamID（RAPID）的组织特异性转录足迹。

跨细胞类型的差异基因表达是多细胞生物中发育和细胞生理的基础。秀丽隐杆线虫是一种功能强大的，广泛使用的模型，可以解决这些生物学问题。然而，仍然存在瓶颈，因为难以获得有效的方法来执行和/或需要大量蠕虫种群，因此难以获得全面的组织特异性基因转录数据。这里，我们引入ř Ñ甲P醇坝ID（RAPID）的方法，其中，所述坝甲基稠合到一个无处不在的RNA聚合酶亚基以创建转录脚印经由转录基因的DNA上的甲基标记。为了验证该方法，我们通过特异性驱动Dam融合表达，确定了完整动物，分选的胚胎卵裂球以及来自完整年轻成年人的不同组织中的聚合酶足迹。根据整个动物或特定组织中的RNA-seq研究，我们获得了有意义的转录足迹。为了挑战RAPID的敏感性并证明其在确定新型组织特异性转录谱中的效用，我们确定了XXX对神经内分泌细胞对的转录足迹，占动物体细胞含量的0.2％。我们鉴定了2362个候选基因，其在XXX细胞中具有假定的活性转录，其中少数已知标记物可用于这些细胞。使用转录报告子获取新匹配的子集，我们确认其中大多数在XXX中表达，并鉴定出新的XXX特异性标记。综上所述，我们的工作将RAPI​​D建立为一种有效的方法，可用于确定特定组织中聚合酶的足迹。秀丽隐杆线虫无需细胞分选或RNA标记。