PUBLICATION
RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
- Authors
- Shi, B., Zhang, J., Heng, J., Gong, J., Zhang, T., Li, P., Sun, B.F., Yang, Y., Zhang, N., Zhao, Y.L., Wang, H.L., Liu, F., Zhang, Q.C., Yang, Y.G.
- ID
- ZDB-PUB-200520-2
- Date
- 2020
- Source
- Genome biology 21: 120 (Journal)
- Registered Authors
- Liu, Feng
- Keywords
- Elavl1a, RNA structure, Structure-based regulome, Zebrafish early embryogenesis
- Datasets
- GEO:GSE120724
- MeSH Terms
-
- 3' Untranslated Regions
- Animals
- ELAV Proteins/metabolism
- Embryo, Nonmammalian/metabolism*
- Molecular Structure
- RNA/chemistry
- RNA/metabolism*
- RNA Processing, Post-Transcriptional*
- RNA Stability
- Transcriptome*
- Zebrafish/embryology*
- Zebrafish/metabolism
- Zebrafish Proteins/metabolism
- PubMed
- 32423473 Full text @ Genome Biol.
Citation
Shi, B., Zhang, J., Heng, J., Gong, J., Zhang, T., Li, P., Sun, B.F., Yang, Y., Zhang, N., Zhao, Y.L., Wang, H.L., Liu, F., Zhang, Q.C., Yang, Y.G. (2020) RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function. Genome biology. 21:120.
Abstract
Background Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined.
Results Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3' UTR and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppresses Elavl1a's binding leading to the decay of its maternal targets.
Conclusions Our study finds that RNA structurally variable regions are enriched in mRNA 3' UTRs and contain cis-regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping