DNA Methylation and Potential for Epigenetic Regulation in Pygospio elegans

Functional genomics in Spiralia

Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.

Streblospio benedicti: A genetic model for understanding the evolution of development and life-history

Investigating developmental evolution usually requires comparing differences across related species to infer how phenotypic change results from embryological modifications. However, when comparing organisms from different environments, ecologies, and evolutionary histories there can be many confounding factors to finding a genetic basis for developmental differences. In the marine annelid Streblospio benedicti, there are two distinct types of offspring with independent developmental pathways that converge on the same adult phenotype. To my knowledge, S. benedicti is the only known species that has heritable (additive) genetic variation in developmental traits that results in alternative life-history strategies. Females produce either hundreds of small, swimming and feeding larvae, or dozens of large, nonfeeding larvae. The larvae differ in their morphology, ecology, and dispersal potential. This developmental dimorphism makes S. benedicti a unique and useful model for understanding how genetic changes result in developmental modifications that ultimately lead to overall life-history differences. Because the offspring phenotypes of S. benedicti are heritable, we can use forward genetics within a single evolutionary lineage to disentangle how development evolves, and which genes and regulatory mechanisms are involved.

DNA methylation atlas and machinery in the developing and regenerating annelid Platynereis dumerilii

BACKGROUND

Methylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and constitutes the basis for mechanisms regulating multiple aspects of embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation of promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the nucleosome remodeling and deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. However, less is known about regulatory mechanisms involving 5mC methylation and their function in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid worm Platynereis dumerilii, an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body post-amputation.

RESULTS

Using in silico and experimental approaches, we show that P. dumerilii displays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation in P. dumerilii is dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly single-copy genes encoding the machinery associated with 5mC methylation or members of the NuRD complex in P. dumerilii and show that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed during P. dumerilii development and regeneration. Treatment with the DNA hypomethylating agent Decitabine impairs P. dumerilii larval development and regeneration and has long-term effects on post-regenerative growth.

CONCLUSIONS

Our data reveal high levels of 5mC methylation in the annelid P. dumerilii, highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation in P. dumerilii development and regeneration. We also present data indicating that P. dumerilii constitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.

Understanding 'Non-genetic' Inheritance: Insights from Molecular-Evolutionary Crosstalk

Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.

De novo transcriptome assembly and developmental mode specific gene expression of Pygospio elegans

Species with multiple different larval developmental modes are interesting models for the study of mechanisms underlying developmental mode transitions and life history evolution. Pygospio elegans, a small, tube-dwelling polychaete worm commonly found in estuarine and marine habitats around the northern hemisphere, is one species with variable developmental modes. To provide new genomic resources for studying P. elegans and to address the differences in gene expression between individuals producing offspring with different larval developmental modes, we performed whole transcriptome Illumina RNA sequencing of adult worms from two populations and prepared a de novo assembly of the P. elegans transcriptome. The transcriptome comprises 66,233 unigenes, of which 33,807 contain predicted coding sequences, 26,448 have at least one functional annotation, and 3,076 are classified as putative long non-coding RNAs. We found more than 8,000 unigenes significantly differentially expressed between adult worms from populations producing either planktonic or benthic larvae. This comprehensive transcriptome resource for P. elegans adds to the available genomic data for annelids and can be used to uncover mechanisms allowing developmental variation in this and potentially other marine invertebrate species.