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Epigenetic machinery is functionally conserved in cephalopods.

Filippo Macchi1, Eric Edsinger2, Kirsten C Sadler3

  • 1Program in Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.

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|September 14, 2022
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Summary

Cephalopod epigenetics reveal conserved DNA methylation and histone modification machinery. In octopus, DNA methylation enriches gene bodies, not transposons, potentially regulating tissue-specific gene expression.

Keywords:
CephalopodsDNA methylationDNMT1EpigeneticsHistone methylationOctopus bimaculoidesUHRF1

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Area of Science:

  • Molecular Biology
  • Genetics
  • Evolutionary Biology

Background:

  • Epigenetic regulatory mechanisms vary across the animal kingdom but are understudied in non-model organisms.
  • Cephalopods possess unique features relevant to behavioral, sensory, developmental, and regenerative processes.
  • The role of epigenetics in regulating these unique cephalopod features remains largely unknown.

Purpose of the Study:

  • To investigate the presence and pattern of DNA methylation in cephalopods.
  • To examine DNA methylation and three histone post-translational modifications across different tissues in three cephalopod species.
  • To understand the role of epigenetic regulation in cephalopod biology.

Main Methods:

  • Bioinformatic and molecular analysis of Octopus bimaculoides.
  • Analysis of DNA methylation and histone modifications (H3K27me3, H3K9me3, H3K4me3) across tissues.
  • Whole genome bisulfite sequencing and reduced representation bisulfite sequencing.

Main Results:

  • Dynamic expression of epigenetic regulators, including DNA methylation maintenance factors, was observed in octopus tissues.
  • Levels of 5-methyl-cytosine were lower in cephalopods compared to vertebrates.
  • DNA methylation in octopus was enriched in gene bodies of a subset of genes and absent from transposons, with distinct patterns observed for hypermethylated and hypomethylated genes.

Conclusions:

  • The epigenetic machinery involving DNA methylation and histone modifications is conserved in cephalopods.
  • In octopus, DNA methylation is associated with gene bodies of highly expressed genes, not transposons.
  • Epigenetic mechanisms, including DNA methylation and histone modifications, likely cooperate to regulate tissue-specific gene expression in cephalopods.