m⁶A Profile Dynamics Indicates Regulation of Oyster Development by m⁶A-RNA Epitranscriptomes

Area of Science:

• Molecular Biology
• Developmental Biology
• Genomics

Background:

• N⁶-methylation of RNA adenosines (m⁶A) is a key regulator of gene expression in vertebrates and insects.
• The role of epitranscriptomes in lophotrochozoan development is largely unknown.
• Oysters serve as a model organism to investigate lophotrochozoan development.

Purpose of the Study:

• To investigate the developmental significance of epitranscriptomes in oysters.
• To characterize the dynamic transcriptome-wide m⁶A methylomes throughout oyster development.
• To understand the relationship between m⁶A modification and gene expression during development.

Main Methods:

• Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was employed.
• Transcriptome-wide m⁶A-RNA methylomes were generated from oyster oocytes to juveniles.
• Bioinformatic analyses were used to correlate methylation profiles with developmental stages and gene functions.

Main Results:

• Oyster RNA classes (mRNAs, lncRNAs, TEs) exhibit distinct m⁶A signatures.
• Epitranscriptomes are dynamic, with methylation levels changing across developmental stages (cleavage, gastrulation, organogenesis, metamorphosis).
• mRNA m⁶A levels correlate with transcript levels and developmental functions, while TE transcript methylation peaks during gastrulation.

Conclusions:

• m⁶A-RNA methylomes are dynamic and regulate gene expression during oyster development.
• The findings provide insights into the control and evolution of developmental processes in lophotrochozoans.
• This study elucidates the epitranscriptome's role in cleavage, maternal-to-zygotic transition, and cell differentiation.