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Series GSE89420 Query DataSets for GSE89420
Status Public on Feb 01, 2018
Title Surveillance of rRNA synthesis by an RNA helicase mediates tissue-specific developmental disorders
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Myriad of craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as ribosome biogenesis. While it is understood that many of these highly tissue-specific malformations are a consequence of defects in cranial neural crest cells (cNCCs), an embryonic cell group that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell type-selectivity of these effects remains largely unknown. Here we show that DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I and Pol II dependent transcriptional arms of ribosome biogenesis, is a key mediator of the nucleolar stress response. Using an in vitro model of Treacher Collins Syndrome (TCS), a craniofacial disorder caused by heterozygous mutations in components of the Pol I transcriptional machinery, we demonstrate that perturbations in ribosomal RNA (rRNA) transcription induce DDX21-mediated surveillance mechanism in cNCCs, leading to DDX21 relocalization from the nucleolus to the nucleoplasm, its eviction from Pol I and Pol II chromatin targets and inhibition of rRNA processing. Importantly, these effects are cell type-selective, cell-autonomous and involve activation of the p53 pathway. We further show that cNCCs are characterized by the inherently high reservoir of p53 mRNA and sensitivity to p53-mediated apoptosis. Remarkably, preventing the loss of DDX21 from nucleolus and chromatin can rescue both the sensitivity to apoptosis and TCS-associated craniofacial phenotypes in vivo. This mechanism is not restricted to TCS, as gene function perturbations linked to other ribosomopathies with craniofacial manifestations also lead to the activation of DDX21 surveillance. Lastly, we provide evidence that inhibition of rRNA synthesis leads to rDNA damage, and furthermore, that rDNA damage is sufficient to activate DDX21 surveillance and elicits tissue-selective and dosage-dependent effects on craniofacial development in vivo.
 
Overall design Examination of DDX21 and TCOF1 binding to chromatin

Examination of DDX21 irCLIP from HeLa with DMSO or ActD treatments
 
Contributor(s) Calo E, Wysocka J
Citation(s) 29364875
Submission date Nov 02, 2016
Last update date May 15, 2019
Contact name Eliezer Calo
E-mail(s) ecalolab@gmail.com
Organization name Massachusetts Institute of Technology
Department Biology
Lab calo
Street address 31 Ames St, 68-270A
City Cambridge
State/province MASSACHUSETTS
ZIP/Postal code 02139
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM2371331 HeLa DDX21 ChIP-seq
GSM2371332 HeLa DDX21 ChIP-seq in iPol I treated cells
GSM2371333 HeLa DDX21 ChIP-seq in siTCOF1
Relations
BioProject PRJNA352129
SRA SRP092428

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89420_HS_HeLa_irCLIP_DDX21_ActD_minus.bw 1.3 Mb (ftp)(http) BW
GSE89420_HS_HeLa_irCLIP_DDX21_ActD_plus.bw 1.4 Mb (ftp)(http) BW
GSE89420_HS_HeLa_irCLIP_DDX21_DMSO_minus.bw 1.2 Mb (ftp)(http) BW
GSE89420_HS_HeLa_irCLIP_DDX21_DMSO_plus.bw 1.3 Mb (ftp)(http) BW
GSE89420_RAW.tar 41.9 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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