|
Status |
Public on Nov 15, 2018 |
Title |
Spatio-temporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline |
Organism |
Caenorhabditis elegans |
Experiment type |
Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing
|
Summary |
In animal germlines, regulation of cell proliferation and differentiation is particularly important but poorly understood. Here, using a cryo-cut approach, we mapped RNA expression along the Caenorhabditis elegans germline and, using mutants, dissected gene regulatory mechanisms that control spatio-temporal expression. We detected, at near single-cell resolution, > 10,000 mRNAs, > 300 miRNAs and numerous unannotated miRNAs. Most RNAs were organized in distinct spatial patterns. Germline-specific miRNAs and their targets were co-localized. Moreover, we observed differential 3’ UTR isoform usage for hundreds of mRNAs. In tumorous gld-2 gld-1 mutants, gene expression was strongly perturbed. In particular, differential 3’ UTR usage was significantly impaired. We propose that PIE-1, a transcriptional repressor, functions to maintain spatial gene expression. Our data also suggest that cpsf-4 and fipp-1 control differential 3’ UTR usage for hundreds of genes. Finally, we constructed a “virtual gonad” enabling “virtual in situ hybridizations” and access to all data (https://shiny.mdc-berlin.de/spacegerm/).
|
|
|
Overall design |
Investigation of the spatio-temporal gene expression in the Caenorhabditis elegans germline using a cryo-based approach and single cell protocols.
|
|
|
Contributor(s) |
Diag A, Schilling M, Klironomos F, Ayoub S, Rajewsky N |
Citation(s) |
30416012 |
|
Submission date |
Jun 15, 2018 |
Last update date |
Jan 27, 2019 |
Contact name |
Nikolaus Rajewsky |
E-mail(s) |
rajewsky@mdc-berlin.de
|
Phone |
+49 30 9406-2998
|
Organization name |
Max Delbrück Center for Molecular Medicine
|
Department |
Berlin Institute for Medical Systems Biology
|
Lab |
Systems Biology of Gene Regulatory Elements
|
Street address |
Robert-Rössle-Straße 10
|
City |
Berlin |
State/province |
Berlin |
ZIP/Postal code |
13125 |
Country |
Germany |
|
|
Platforms (3) |
GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
GPL22765 |
Illumina HiSeq 4000 (Caenorhabditis elegans) |
|
Samples (97)
|
|
Relations |
BioProject |
PRJNA476356 |
SRA |
SRP150643 |