Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Area of Science:

• Molecular Biology
• Developmental Biology
• Genetics

Background:

• RNA structure is vital for function, but dynamic changes during biological transitions are poorly understood.
• Existing knowledge of transcriptome-wide RNA structure is limited to steady-state conditions.
• Understanding RNA structure dynamics is crucial for deciphering gene function during development.

Purpose of the Study:

• To characterize messenger RNA (mRNA) structure dynamics during zebrafish development.
• To investigate the interplay between translation and RNA structure in vivo.
• To explore the role of 3' untranslated regions (UTRs) in gene regulation during development.

Main Methods:

• In vivo characterization of mRNA structure dynamics.
• Analysis of RNA structure in translated and untranslated regions.
• Identification of RNA structure remodeling factors.

Main Results:

• Global mRNA structure is primarily guided by translation, not the reverse.
• Translated regions exhibit decreased RNA structure, with ribosomes acting as key remodelers.
• 3' UTRs form stable, folded structures in vivo, influencing microRNA activity and containing RNA-decay elements.
• Dynamic 3' UTR structures are implicated in regulating maternal factors during the maternal-to-zygotic transition.

Conclusions:

• RNA structure dynamics play a central role in gene regulatory programs during development.
• Ribosomes actively remodel mRNA structure during translation.
• 3' UTR structural dynamics are critical for controlling gene expression and developmental timing.