7SK is a highly conserved non-coding RNA that regulates eukaryotic transcription by sequestering positive transcription elongation factor b (P-TEFb). 7SK regulatory function likely entails changes in RNA structure, but characterizing dynamic RNA-protein complexes in cells has remained an unsolved challenge. We describe a new chemical probing strategy (DANCE-MaP) that uses maximum likelihood deconvolution and probabilistic read assignment to define simultaneously (i) per-nucleotide reactivity profiles, (ii) direct base pairing interactions, and (iii) tertiary and higher-order interactions for each conformation of multi-state RNA structural ensembles, all from a single experiment. We show that human 7SK RNA, despite significant heterogeneity, intrinsically codes for a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium is regulated by cell type, shifts dynamically in response to cell growth and stress, and can be exogenously targeted to modulate transcription in cells. Our data support that the 7SK structural ensemble functions as an integrator of diverse cellular signals to control transcription elongation in environment and cell specific ways, and establishes DANCE-MaP as a powerful strategy for comprehensively defining RNA structure and dynamics in cells.

中文翻译：

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7SK RNA 中的大规模变构开关调节转录以响应生长和压力

7SK 是一种高度保守的非编码 RNA，它通过隔离正转录延伸因子 b (P-TEFb) 来调节真核转录。7SK 调节功能可能需要改变 RNA 结构，但表征细胞中动态的 RNA-蛋白质复合物仍然是一个悬而未决的挑战。我们描述了一种新的化学探测策略 (DANCE-MaP)，它使用最大似然解卷积和概率读取分配来同时定义 ( i ) 每核苷酸反应性谱，( ii ) 直接碱基配对相互作用，以及 ( iii)) 多态 RNA 结构集合的每个构象的三级和高级相互作用，全部来自单个实验。我们表明，尽管存在显着的异质性，人类 7SK RNA 本质上编码了大规模结构转换，该转换将 P-TEFb 结合位点的溶解与远端释放因子结合位点的结构重塑相结合。7SK 结构平衡受细胞类型调节，响应细胞生长和压力而动态变化，并且可以外源靶向调节细胞中的转录。我们的数据支持 7SK 结构集合作为多种细胞信号的整合器，以控制环境和细胞特定方式的转录延伸，并将 DANCE-MaP 确立为全面定义细胞中 RNA 结构和动力学的强大策略。