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

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. Overall design: Examination of DDX21 chromatin association and DDX21 RNA interacting partners in HEK293 cells

DEAD-box RNA解旋酶（DEAD-box RNA helicases）对于RNA生命周期诸多环节的调控至关重要，但其参与调控的分子基础，尤其是在哺乳动物细胞中的相关机制，目前仍不甚明晰。本研究发现，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，以及多种类型的编码蛋白RNA与非编码RNA。尽管这类分子相互作用范围广泛，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可结合转录中的核糖体DNA（rDNA）位点，直接接触核糖体RNA（rRNA）与小核仁RNA（snoRNA），并作为小核仁RNA核糖核蛋白（snoRNA ribonucleoprotein，snoRNP）复合物的功能组分，促进核糖体RNA的修饰反应。在核质中，DDX21会整合进入7SK 小核核糖核蛋白（7SK snRNP）复合物，该复合物可促进DDX21与编码核糖体蛋白及小核仁RNA的RNA聚合酶II转录基因的启动子区域相结合。结合于启动子区域的DDX21可促进正性转录延伸因子b（P-TEFb）从7SK snRNP复合物中释放，进而增强RNA聚合酶II的有效延伸过程。综上，本研究提出了一套统一的调控机制，可协调不同核区室中的核糖体基因表达，并首次提供证据表明，哺乳动物RNA解旋酶参与了RNA修饰与RNA聚合酶II延伸的调控过程。实验设计：检测HEK293细胞（HEK293）中DDX21与染色质的结合情况，以及DDX21的RNA互作伴侣分子。