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Series GSE129970 Query DataSets for GSE129970
Status Public on Jun 17, 2019
Title Effects of cadmium and integrator complex knockdown on gene expression and mRNA splicing
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary RNA undergoes numerous processing steps required for gene expression. Little is known about RNA homeostasis during environmental stress in metazoan cells. By studying regulation of a heavy metal-induced gene named numr-1 in C. elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and regulates RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing and causes aberrant pre-mRNA splicing. Cadmium, which also strongly induces numr-1, has the same effects on snRNA processing and pre-mRNA splicing. Lastly, we find that heat shock factor-1 is required for numr-1 induction by cadmium. Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1.
 
Overall design We report the use of mRNA sequencing to analyze the effects of cadmium exposure and integrator complex gene knockdown have on the transcriptome.
Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq with Alternative splicing data analyzed by rMATS.
 
Contributor(s) Wu CW, Choe KP, Wimberly K
Citation(s) 31311534
Submission date Apr 17, 2019
Last update date Jul 29, 2019
Contact name Cheng-Wei Wu
E-mail(s) michael.wu@usask.ca
Phone 306-966-7672
Organization name University of Saskatchewan
Street address 52 Campus Drive
City Saskatoon
State/province SK
ZIP/Postal code S7N 5B4
Country Canada
 
Platforms (1)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (18)
GSM3728761 N2_empty vector_control_rep1
GSM3728762 N2_empty vector_control_rep2
GSM3728763 N2_empty vector_control_rep3
Relations
BioProject PRJNA533307
SRA SRP192875

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE129970_emptyvector_control_cadmium.xlsx 3.0 Mb (ftp)(http) XLSX
GSE129970_ints-4_cadmium.xlsx 3.1 Mb (ftp)(http) XLSX
GSE129970_ints-4_control.xlsx 3.2 Mb (ftp)(http) XLSX
GSE129970_numr-1_cadmium.xlsx 3.1 Mb (ftp)(http) XLSX
GSE129970_numr-1_control.xlsx 3.0 Mb (ftp)(http) XLSX
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Processed data are available on Series record

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