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Series GSE56802 Query DataSets for GSE56802
Status Public on Nov 17, 2014
Title RNA helicase DDX21 coordinates transcription and noncoding RNA processing of the ribosomal pathway
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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
Contributor(s) Calo E, Flynn RA, Chang HY, Wysocka J
Citation(s) 25470060
Submission date Apr 15, 2014
Last update date May 15, 2019
Contact name Ryan Alexander Flynn
Organization name Stanford University
Street address 380 Roth Way, Room 265
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM1369392 DDX21-ChIPSeq
GSM1369393 Input DNA
GSM1369394 DDX21 iCLIP Biological replicate 1
BioProject PRJNA244630
SRA SRP041180

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Supplementary file Size Download File type/resource 164.2 Kb (ftp)(http) BW 719.5 Kb (ftp)(http) BW
GSE56802_RAW.tar 102.1 Mb (http)(custom) TAR (of BEDGRAPH, WIG)
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