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RNA sequencing of DDX23 knockdown by siRNA in ovarian cancer cells

ABSTRACT: DDX23 belongs to DEAD-box family of RNA helicases and plays crucial roles in spliceosome formation and pre-mRNA splicing. In this study, DDX23 was first identified as a key DEAD-box RNA helicase in ovarian cancer, and its overexpressed was associated with poor clinical outcomes. High expression of DDX23 was involved in the malignant proliferation and aggressiveness of ovarian cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE181078 | GEO | 2021/07/31

REPOSITORIES: GEO

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Transcriptional profile analysis of uninfected or VSV-infected scrambled siRNA (siControl) and DDX23 knockdown (siDDX23) A549 cells

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The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism

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Project description: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

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