RNA helicase DDX21 coordinates transcription and ribosomal RNA processing
RNA helicase DDX21 coordinates transcription and ribosomal RNA processing
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 the transcriptional status of both RNA polymerase (Pol) I and II to control multiple 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 RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.
- Stanford University United States
- University of California, San Francisco United States
Transcription, Genetic, 3102 Bioinformatics and Computational Biology (for-2020), General Science & Technology (science-metrix), Post-Transcriptional, Small Nucleolar (mesh), DEAD-box RNA Helicases, RNA Polymerase I, Protein Binding (mesh), Positive Transcriptional Elongation Factor B, rRNA, RNA Processing, Post-Transcriptional, Humans (mesh), Chromatin (mesh), Ribosomal (mesh), Generic health relevance (hrcs-hc), RNA-Binding Proteins, Biological Sciences, Ribonucleoproteins, Small Nuclear, Chromatin, Ribonucleoproteins, RNA Polymerase II, Transcription, Post-Transcriptional (mesh), Protein Binding, 570, RNA Processing, General Science & Technology, 1.1 Normal biological development and functioning, Bioinformatics and Computational Biology, Small Nuclear, Genetic, DEAD-box RNA Helicases (mesh), 616, Genetics, Humans, RNA, Small Nucleolar, RNA Polymerase I (mesh), Small Nucleolar, Ribosomal, 1.1 Normal biological development and functioning (hrcs-rac), Small Nuclear (mesh), 31 Biological Sciences (for-2020), Genetics (rcdc), Positive Transcriptional Elongation Factor B (mesh), RNA Polymerase II (mesh), Genes, rRNA, rRNA (mesh), RNA-Binding Proteins (mesh), Genes, RNA, Ribosomal, RNA, Genetic (mesh), Generic health relevance
Transcription, Genetic, 3102 Bioinformatics and Computational Biology (for-2020), General Science & Technology (science-metrix), Post-Transcriptional, Small Nucleolar (mesh), DEAD-box RNA Helicases, RNA Polymerase I, Protein Binding (mesh), Positive Transcriptional Elongation Factor B, rRNA, RNA Processing, Post-Transcriptional, Humans (mesh), Chromatin (mesh), Ribosomal (mesh), Generic health relevance (hrcs-hc), RNA-Binding Proteins, Biological Sciences, Ribonucleoproteins, Small Nuclear, Chromatin, Ribonucleoproteins, RNA Polymerase II, Transcription, Post-Transcriptional (mesh), Protein Binding, 570, RNA Processing, General Science & Technology, 1.1 Normal biological development and functioning, Bioinformatics and Computational Biology, Small Nuclear, Genetic, DEAD-box RNA Helicases (mesh), 616, Genetics, Humans, RNA, Small Nucleolar, RNA Polymerase I (mesh), Small Nucleolar, Ribosomal, 1.1 Normal biological development and functioning (hrcs-rac), Small Nuclear (mesh), 31 Biological Sciences (for-2020), Genetics (rcdc), Positive Transcriptional Elongation Factor B (mesh), RNA Polymerase II (mesh), Genes, rRNA, rRNA (mesh), RNA-Binding Proteins (mesh), Genes, RNA, Ribosomal, RNA, Genetic (mesh), Generic health relevance
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