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| Status |
Public on Aug 01, 2016 |
| Title |
Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 1) |
| Organism |
Schmidtea mediterranea |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Understanding gene regulation in stem cells is key to understanding stem cell biology.Contrary to transcriptional regulation the function of alternative splicing (AS) in stem cells is poorly understood. Here we study function and mechanisms of AS in a powerful in vivo model for stem cell biology, the planarian S. mediterranea. Knockdown of AS factors, computational analyses of massive RNA-sequencing data, phenotyping, and biochemical binding assays revealed a stem cell specific AS program comprising hundreds of alternative exons, intron retention events, and microexons. The conserved AS factors CELF/MBNL are main regulators of this program. We show that they antagonize each other by directly promoting or repressing stem cell specific AS events. Knockdown of CELF/MBNL leads to defective regeneration by affecting self-renewal and differentiation, respectively. Thus, AS is of key importance for stem cell regulation in vivo and antagonistic regulation by CELF/MBNL is likely an ancestral feature of animal stem cells.
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| Overall design |
Sequencing of polyA-selected RNA from Schmidtea mediterranea individuals after control, smed-bruno-like(RNAi) and mbnl(RNAi) after 20,25,30 days after RNAi
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| Contributor(s) |
Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Ray D, Morris QD, Hughes TR, Blencowe BJ, Rajewsky N |
| Citation(s) |
27502555 |
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| Submission date |
Nov 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Marta Rodriguez Orejuela |
| Organization name |
Max Delbruck Centrum
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| Department |
Berlin Institute for Medical Systems Biology
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| Street address |
Robert-Roessle str. 10 (H. 87)
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platforms (1) |
| GPL15553 |
Illumina HiSeq 2000 (Schmidtea mediterranea) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA303146 |
| SRA |
SRP066558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE75296_bruli_mbnl_phenotypic_analysis_tpm.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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