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| Status |
Public on Aug 05, 2019 |
| Title |
Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein rbm14 |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, rbm14's IDR demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from other phase-separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as largescale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.
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| Overall design |
Zebrafish embryo mRNA profiles of ctrl-MO and rbm14-MOs by deep sequencing at 10hpf and 24hpf. For each sample, 50 embryos were pooled.
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| Contributor(s) |
Xiao Y, Chen J |
| Citation |
Yue Xiao, Jiehui Chen, Yihan Wan, Qi Gao, Naihe Jing, Yixian Zheng and Xueliang Zhu. Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein Rbm14. Cell Discovery 2019;5, article number 37. doi:10.1038/s41421-019-0106-xDO
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| Submission date |
Mar 28, 2019 |
| Last update date |
Aug 05, 2019 |
| Contact name |
Yue Xiao |
| E-mail(s) |
xiaoyue@sibcb.ac.cn
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| Organization name |
Shanghai Institute of Biochemistry and Cell Biology
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| Street address |
320 Yue Yang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA529647 |
| SRA |
SRP189736 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128984_RAW.tar |
1.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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