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Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics
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Comparative Transcriptomics to Identify RNA Writers and Erasers in Microalgae.

Luca Ambrosino1, Alessia Riccardi2, Melina S Welling3

  • 1Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy.

International Journal of Molecular Sciences
|August 10, 2024
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Summary
This summary is machine-generated.

This study identified RNA methyltransferases (writers) and demethylases (erasers) in microalgae, revealing their differential expression under nutrient stress. Some writer genes were absent in transcriptomes but present in genomes, indicating condition-specific expression.

Keywords:
epitranscriptomicserasersmicroalgaestress responseswriters

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Area of Science:

  • Epitranscriptomics
  • Molecular Biology
  • Marine Microbiology

Background:

  • Epitranscriptomics represents a novel regulatory layer in eukaryotes, crucial for development and stress adaptation.
  • RNA methyltransferases (writers) and demethylases (erasers) are key players in epitranscriptomic regulation.

Purpose of the Study:

  • To identify RNA writer and eraser enzymes in four microalgal species: *Alexandrium tamutum*, *Amphidinium carterae*, *Cylindrotheca closterium*, and *Tetraselmis suecica*.
  • To investigate the expression patterns of these enzymes under nutrient starvation stress.

Main Methods:

  • Bioinformatic identification of RNA writer and eraser genes using known plant sequences as queries.
  • Genome-wide sequence similarity searches to confirm gene presence.
  • Gene expression analysis under various nutrient stress conditions (nitrogen depletion, phosphate depletion, zinc addition) in *A. carterae*.

Main Results:

  • Most known plant RNA writer and eraser genes were identified in the studied microalgae, with exceptions for MTA, VIRILIZER, and HAKAI.
  • Sequence similarity searches confirmed the presence of MTA, VIRILIZER, and HAKAI in the genomes, suggesting their absence in transcriptomes was due to lack of expression.
  • Differential expression of identified genes was observed under nutrient stress conditions, particularly in *A. carterae*.

Conclusions:

  • Microalgae possess a conserved set of RNA epitranscriptomic machinery similar to plants.
  • The expression of specific RNA writer and eraser genes is regulated by nutrient availability and other environmental stressors.
  • This study provides foundational insights into the role of epitranscriptomics in microalgal stress response and gene regulation.