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Dynamic Expression of the Zebrafish (Danio rerio) Proteome Across Early Larval Development

ABSTRACT: Here, we characterize proteome expression patterns in larval zebrafish at 4-, 7- and 10 dpf using bottom-up shotgun proteomics

INSTRUMENT(S): Synapt G2-S HDMS, ACQUITY UPLC

ORGANISM(S): Danio Rerio (ncbitaxon:7955)

SUBMITTER: Bryan W. Brooks

PROVIDER: MSV000096671 | MassIVE | Mon Dec 16 18:12:00 GMT 2024

SECONDARY ACCESSION(S): PXD058917

REPOSITORIES: MassIVE

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Project description:The transgenerational inheritance of epigenetic information is an attractive mechanism by which the phenotypic consequences of exposure of parents to certain environmental conditions could be transmitted to the next generation. Although this phenomenon is well described in yeast and plants, and in some invertebrates, such as the D. melanogaster and C. elegans, the evidence for transgenerational inheritance in vertebrates is scarce. Among the mechanisms that are known or suspected to be involved in mediating the propagation of epigenetic information to subsequent generations, the process of enzymatic DNA methylation is of particular interest. During DNA replication, the methylation pattern of the parental strand is faithfully copied onto the daughter strand by the maintenance methylase DNMT1, although methylation patterns can be changed through the action of de novo methylases and mechanisms of active and passive demethylation. In the context of epigenetic inheritance, the induction of aberrant methylation patterns in gametes may set the stage for transmission into future generations. Here, we describe a viable hypomorphic allele of dnmt1 in zebrafish that causes widespread demethylation of CpG dinucleotides in sperm and somatic tissues. Surprisingly, homozygous mutants present with an essentially normal phenotype, with the exception of drastically impaired lymphopoiesis, affecting both larval and adult phases of T cell development. Male but not female mutants are fertile. The phenotype of impaired larval (but not adult) T cell development is transmitted to subsequent generations by about 50% of fish that are genotypically wildtype. Whole genome bisulfite sequencing of sperm DNA of transmitting and non-transmitting males identified about 200 differentially methylated regions, including hypermethylated sites associated with runx3 and rptor genes. Knock-down of these two genes leads to impaired larval T cell development. Our results raise the possibility of an epigenetic origin of certain immunodeficiency syndromes in animals and humans.

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Dynamic Expression of the Zebrafish (Danio rerio) Proteome Across Early Larval Development

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