DNA and coding/non-coding RNA methylation analysis provide insights into tomato fruit ripening.

Area of Science:

• Plant Biology
• Molecular Biology
• Epigenetics

Background:

• Fruit ripening is a critical developmental stage for palatability and seed dispersal.
• N6-methyladenosine (m5C) is an important epitranscriptomic modification influencing gene expression.
• Understanding m5C dynamics in fruit ripening is crucial for improving fruit quality and storage.

Purpose of the Study:

• To investigate the role of m5C modification in the ripening process of 'Alisa Craig' fruit.
• To identify m5C-modified mRNAs and their involvement in stress response and cell wall metabolism during ripening.
• To explore the relationship between m5C methylation, mRNA expression, and key ripening regulatory pathways.

Main Methods:

• Transcriptome-wide analysis of m5C modification in fruit tissues.
• Differential gene expression analysis combined with methylation profiling.
• Identification of m5C targets, including mRNAs, long non-coding RNAs, and circular RNAs.

Main Results:

• Increased m5C levels were observed in mRNAs related to stress response (e.g., STPK, WRKY 40) and cell wall metabolism (e.g., PG, EXP-B1).
• The 'Nr' mutant exhibited altered m5C modification in ripening-associated mRNAs (WRKY, MADS-box).
• Combined analysis revealed differentially expressed genes with differential methylation, including transcription factors (e.g., ERF084, EIN3, AP2/ERF) and ethylene pathway components (e.g., ACO5, ACS7, ETR1).

Conclusions:

• m5C modification plays a significant role in regulating gene expression during fruit ripening.
• m5C-modified RNAs are involved in stress responses, cell wall modifications, and ethylene signaling pathways crucial for ripening.
• These findings enhance the understanding of fruit ripening mechanisms and provide insights for post-harvest management.