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Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies

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The Molecular Life of Diatoms

Abstract

Epigenetics and its role in genome regulation is one of the most exciting areas of modern science. After a brief history of epigenetics and an introduction to the molecular basics of this discipline of science, this chapter describes the current knowledge of epigenetic components in diatoms, namely writers and erasers of DNA methylation and histone modifications. With a particular focus on the model pennate diatom Phaeodactylum tricornutum, we describe our current understanding of the contribution of few epigenetic factors to diatoms biology. Further, short regulatory non-coding RNAs (ncRNAs) as well as long ncRNAs are described in light of recent research. We highlight future studies and directions with a focus on epigenomic editing and environmental epigenetics.

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Abbreviations

5mC:

5-methylcytosine

ALKBH:

alpha-ketoglutarate-dependent hydroxylase

COLDAIR :

COLD ASSISTED INTRONIC NONCODING RNA

DCL:

Dicer endonuclease

DEXDc/Helicase:

Dead like helicase domain

DME:

DEMETER

DNA:

Deoxyribonucleic acid

DNMTs:

DNA methyltransferases

DUF:

Domain of unknown function

ENDO3c:

Endonuclease IIIc

FLC:

Flowering Locus C

HDACs:

Histone deacetylases

HDMs:

Histone demethylases

LncRNAs:

Long non-coding RNAs

miRNA:

micro RNAs

MMETSP:

Marine Microbial Eukaryote Transcriptome Project

PAZ:

Piwi-Argonaute-Zwille

PTMs:

Post-translational modifications of histones

RDRs:

RNA-dependent RNA polymerases

RID/DMTA:

RIP deficient/DNA methyltransferase activity

RIP:

Repeat-induced point mutation

RISC:

RNA-induced silencing complex

RNA:

Ribonucleic acid

ROS:

Reactive oxygen species

SAM:

S-adenosyl-methionine

siRNA:

small interfering RNAs

SNF:

Sucrose non-fermentable

TEs:

Transposable elements

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  1. Xue Zhao and Antoine Hoguin contributed equally with all other contributors.

Authors and Affiliations

  1. Nantes Université, CNRS, US2B, UMR 6286, Nantes, France

    Xue Zhao, Antoine Hoguin, Timothée Chaumier & Leila Tirichine

  2. Département de biologie, École normale supérieure, Institut de Biologie de l’ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France

    Antoine Hoguin

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  1. Xue Zhao
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Correspondence to Leila Tirichine .

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  1. Laboratoire de Biologie du chloroplaste et perception de la lumière chez les microalgues, UMR7141, Centre national de la recherche scientifique, Sorbonne Université Institut de Biologie Physico-Chimique, Paris, France

    Angela Falciatore

  2. School of Environmental Sciences, University of East Anglia Norwich Research Park, Norwich, UK

    Thomas Mock

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Zhao, X., Hoguin, A., Chaumier, T., Tirichine, L. (2022). Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies. In: Falciatore, A., Mock, T. (eds) The Molecular Life of Diatoms. Springer, Cham. https://doi.org/10.1007/978-3-030-92499-7_7

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