Abstract
Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average ~90% of sequence similarities with mice and ~96% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta. The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.
Highlights
Epigenetic modifications are good candidates to explain rapid, inheritable and reversible phenotypes without changes in the deoxyribonucleic acid (DNA) sequence (Danchin et al, 2011). They range from chemical modifications of DNA, covalent changes of proteins participating to chromatin structure, as well as nuclear localization of chromosomes, and non-coding RNAs involved in post-transcriptional silencing of genes and repeated regions
We counted the number of intact Symbiodiniaceae and intact coral nuclei
The low amount of contamination with Symbiodiniaceae was confirmed by whole genome bisulfite sequencing (WGBS), in another experiment from our group using the extraction technique presented in this article: less than 0.004% of the total reads aligned to the S. minutum and S. kawagutii genomes, which are known to compose the Symbiodiniaceae clades in our P. acuta population (Vidal-Dupiol et al, 2019)
Summary
Epigenetic modifications are good candidates to explain rapid, inheritable and reversible phenotypes without changes in the deoxyribonucleic acid (DNA) sequence (Danchin et al, 2011) They range from chemical modifications of DNA (e.g. cytosine methylation), covalent changes of proteins participating to chromatin structure (e.g. histone modifications), as well as nuclear localization of chromosomes, and non-coding RNAs involved in post-transcriptional silencing of genes and repeated regions. In natural populations with genetic diversity, disentangling the respective roles of genetics and epigenetics in environmentally triggered phenotypes is hardly feasible, if not impossible, except with biological models with asexual reproduction This rare feature is one of the characteristics of colonial organisms, such as corals, and they have been used as a model to address such questions. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure
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