Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer

ABSTRACT: The germ layer concept has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years. Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. The origin of the ectoderm and endoderm layers, however, remains unclear with models supporting the antecedence of each as well as a simultaneous origin. We hypothesized that global analysis of gene expression in each layer throughout development may resolve the early events of animal evolution. Here, we determine the temporal and spatial components of gene expression spanning embryonic development for all C. elegans genes and use it to determine the evolutionary age of the germ layers. The gene expression programs of the mesoderm is generally induced after the ectoderm and endoderm germ layers, thus making it the last germ layer to both evolve and develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier. We also observed early expression of endoderm orthologs during the embryology of Xenopus tropicalis, Nematostella vectensis, and the sponge Amphimedon queenslandica. Querying for the phylogenetic ages of specifically expressed genes revealed that the endoderm is comprised of older genes, supporting its antecedence among the germ layers. Taken together, we propose that the endoderm program has retained the feeding functions of the last common ancestor with the choanoflagellates, thus allowing for the specialization of an ectoderm germ layer. Our work reveals that the evolutionary appearance of the germ layers continues to constrain regulatory networks in metazoans. Two temporal assays of C. elegans embryonic development, starting at the zygote: (a) Embryos collected at fixed (~10 minute) time intervals. (b) Embryo segregates, up to five lines of blastomeres, isolated in reference to mitotic events. There were 184 samples in total, representing 100 distnict data points.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Itai Yanai

PROVIDER: E-GEOD-50548 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer.

Hashimshony Tamar T Feder Martin M Levin Michal M Hall Brian K BK Yanai Itai I

Nature 20141210 7542

The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years (refs 1 - 3). Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the ...[more]

PMID: 25487147

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Project description:Embryogenesis is tightly regulated by multiple levels of epigenetic systems such as DNA methylation, histone modification, and chromatin remodeling. DNA methylation patterns are erased in primordial germ cells and in the interval immediately following fertilization. Subsequent reprogramming occurs by de novo methylation and demethylation. Variance of DNA methylation patterns between different cell types is not well understood. Here, using methylated DNA immunoprecipitation and tiling array technology, we have comprehensively analysed DNA methylation patterns at proximal promoter regions in mouse embryonic stem (ES) cells, ES cell-derived early germ layers (ectoderm, endoderm and mesoderm) and four adult tissues (brain, liver, skeletal muscle and sperm). Most of the methylated regions in the three germ layers and in the three adult somatic tissues are shared in common. This commonly methylated gene set is enriched in germ cell associated genes that are generally transcriptionally inactive in somatic cells. We also compared DNA methylation patterns with global mapping of histone H3 lysine 4/27 trimethylation, and found that gain of DNA methylation correlates with loss of histone H3 lysine 4 trimethylation. Taken together, our findings indicate that differentiation from ES cells to the three germ layers is accompanied by an increase in the number of commonly methylated DNA regions and that these tissue-specific alterations are present for only a small number of genes. Our findings indicate that DNA methylation at the proximal promoter regions of commonly methylated genes act as an irreversible mark which fixes somatic lineage by repressing transcription of germ cell specific genes. Using the MeDIP on chip protocol, we immunoprecipitated methylated DNA from R1 ES cell, SK7 cell, as well as SK7 derived-Ectoderm, - Endoderm, -Paraxial mesoderm, brain, liver, skeletal muscle, and sperm, and hybridized to a genome tiling array. The three germ layer lineages from ES cells were confirmed by the expression of specific marker genes in each germ layer (see related expression analysis).

Dataset Information

Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer

Publications

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer.

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