Chovatiya Gopal, Wang Alex B, Versluis Philip, Bai Chris K, Huang Sean Y, DeBerardine Michael, Ray Judhajeet, Ozer Abdullah, Lis John T, Tumbar Tudorita
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
bioRxiv. 2024 Oct 18:2024.10.15.618417. doi: 10.1101/2024.10.15.618417.
Gene regulatory mechanisms that modulate RNA Polymerase II activity are difficult to access in mammalian tissues composed of multiple cell lineages. Here, we develop a nascent RNA assay (PReCIS-seq) that measures lineage-specific transcriptionally-engaged Pol II on genes and DNA enhancer elements in intact mouse tissue. By employing keratinocytes as a prototype lineage, we unearth Pol II promoter-recruitment versus pause-release mechanisms operating in adult skin homeostasis. Moreover, we relate active enhancer proximity and transcription factor binding motifs on promoters to Pol II activity and promoter-proximal pausing level. Finally, we find Pol II firing rapidly into elongation on lineage identity genes and highly paused on cellular safeguarding genes in a context-dependent manner. Our work provides a basic platform to investigate mechanistic principles of gene regulation in individual lineages of complex mammalian tissues.
在由多种细胞谱系组成的哺乳动物组织中，调节RNA聚合酶II活性的基因调控机制很难进行研究。在此，我们开发了一种新生RNA检测方法（PReCIS-seq），该方法可测量完整小鼠组织中基因和DNA增强子元件上谱系特异性转录相关的Pol II。通过将角质形成细胞作为原型谱系，我们揭示了在成年皮肤稳态中起作用的Pol II启动子招募与暂停释放机制。此外，我们将启动子上的活性增强子接近度和转录因子结合基序与Pol II活性和启动子近端暂停水平联系起来。最后，我们发现Pol II在谱系身份基因上迅速进入延伸阶段，并以依赖于上下文的方式在细胞保护基因上高度暂停。我们的工作为研究复杂哺乳动物组织中单个谱系的基因调控机制原理提供了一个基础平台。
