RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway

DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense transcriptional status of both RNA Pol I and Pol II to control transcriptional and post-transcriptional steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of protein-coding and noncoding RNAs. Although broad, these molecular interactions, both at the chromatin and at the RNA level, exhibit a remarkable specificity for the ribosomal pathway. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs and, as a functional component of the snoRNA ribonucleoprotein (snoRNP) complex, promotes modification of rRNA. In the nucleoplasm, DDX21 is incorporated into the 7SK snRNP complex, which facilitates DDX21 association with promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of P-TEFb from the 7SK snRNP, enhancing productive Pol II elongation. Altogether, we present a unifying mechanism for the coordinated regulation of ribosomal genes across nuclear compartments, and provide first evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control. Examination of DDX21 chromatin association and DDX21 RNA interacting partners in HEK293 cells

DEAD-box RNA解旋酶（DEAD-box RNA helicase）在调控RNA生命周期的诸多关键环节中发挥核心作用，但其参与调控的分子基础，尤其是在哺乳动物细胞中的具体机制，目前仍未得到充分阐明。本研究证实，DEAD-box RNA解旋酶DDX21可感知RNA聚合酶I（RNA Pol I）与RNA聚合酶II（RNA Pol II）的转录状态，进而调控人类细胞内核糖体生物发生的转录及转录后步骤。研究表明，DDX21可广泛结合RNA聚合酶I与RNA聚合酶II转录的基因，以及多种编码蛋白的RNA与非编码RNA。尽管这类分子相互作用覆盖范围广泛，但无论是在染色质层面还是RNA层面，均对核糖体通路表现出显著的特异性。在核仁中，DDX21定位于转录中的核糖体DNA（rDNA）位点，可直接结合核糖体RNA（rRNA）与小核仁RNA（snoRNA），并作为小核仁RNA核糖核蛋白（snoRNP）复合物的功能组分，促进rRNA的修饰过程。在核质中，DDX21可整合进入7SK小核核糖核蛋白（7SK snRNP）复合物，这一过程助力DDX21与编码核糖体蛋白及snoRNA的RNA聚合酶II转录基因的启动子区域结合。结合于启动子的DDX21可促进正转录延伸因子b（P-TEFb）从7SK snRNP复合物中释放，增强具有转录活性的RNA聚合酶II的延伸能力。综上，本研究提出了一套统一的调控机制，可实现跨核区室的核糖体基因协同调控，并首次提供证据表明哺乳动物RNA解旋酶参与RNA修饰及RNA聚合酶II延伸调控过程。本研究在HEK293细胞中开展了DDX21染色质结合情况及其RNA互作伴侣的相关检测。