PUBLICATION

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

Authors
Beaudoin, J.D., Novoa, E.M., Vejnar, C.E., Yartseva, V., Takacs, C.M., Kellis, M., Giraldez, A.J.
ID
ZDB-PUB-180801-6
Date
2018
Source
Nature structural & molecular biology   25(8): 677-686 (Journal)
Registered Authors
Giraldez, Antonio, Takacs, Carter M., Vejnar, Charles
Keywords
none
MeSH Terms
  • 3' Untranslated Regions
  • Animals
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks*
  • Nucleic Acid Conformation*
  • Protein Biosynthesis
  • RNA Stability
  • RNA, Messenger/chemistry*
  • RNA, Messenger/genetics
  • Transcriptome
  • Zebrafish/embryology
  • Zebrafish/genetics
PubMed
30061596 Full text @ Nat. Struct. Mol. Biol.
Abstract
RNA folding plays a crucial role in RNA function. However, knowledge of the global structure of the transcriptome is limited to cellular systems at steady state, thus hindering the understanding of RNA structure dynamics during biological transitions and how it influences gene function. Here, we characterized mRNA structure dynamics during zebrafish development. We observed that on a global level, translation guides structure rather than structure guiding translation. We detected a decrease in structure in translated regions and identified the ribosome as a major remodeler of RNA structure in vivo. In contrast, we found that 3' untranslated regions (UTRs) form highly folded structures in vivo, which can affect gene expression by modulating microRNA activity. Furthermore, dynamic 3'-UTR structures contain RNA-decay elements, such as the regulatory elements in nanog and ccna1, two genes encoding key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping