Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Bulk RNA-seq of PSCs and induced PSM cells from six different mammalian species

ABSTRACT: In this study, we performed bulk RNA-seq of pluripotent stem cells (PSCs) and induced pre-somitic mesoderm (PSM) cells of six different mammalian species. The species studied are: mouse (Mus musculus), marmoset (Callithrix jacchus), rabbit (Oryctolagus cuniculus), human (Homo sapiens), cattle (Bos taurus) and southern white rhinoceros (Ceratotherium simum). We used mouse ESCs, marmoset iPSCs, rabbit ESCs, human iPSCs, bovine ESCs and rhinoceros ESCs to induce PSM-like cells from these species following protocols already described. PSC samples were extracted under maintenance conditions. PSM samples were extracted on the day when the differentiation efficiency was higher based on the percentage of cells expressing the PSM marker TBX6. We used identical culture conditions when extracting the induced PSM cells to minimize the effect of external factors on our results. Two replicates per each cell type and species were collected for a total of 24 samples. We compared the expression levels of more than 10,000 orthologous protein-coding genes across the six species. With this, we determined that the species-specific segmentation clock periods might be derived from species-specific gene expression profiles controlling basic biological processes.

INSTRUMENT(S): Illumina NextSeq 500

ORGANISM(S): Oryctolagus cuniculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-12263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Within a given vertebrate species, the total number of vertebrae in each anatomical domain is precisely defined and shows little variation among individuals. In contrast, this number can vary tremendously between different species, ranging from as few as six vertebrae in frogs to as many as several hundred in some snakes and fish. Segmental precursors of the vertebrae, called somites are produced sequentially in the embryo from the presomitic mesoderm (PSM), until a final number characteristic of the species, is reached. Here, we show in the chicken embryo that, by controlling the rate of axis elongation, Hox genes control the total number of somites generated by the embryo. We observed that activation of the most posterior Hox genes in somite precursors of the tail bud correlates with an abrupt slowing-down of the speed of axis elongation. We show that progressively more posterior Hox genes, which are collinearly activated in somitic precursors of the epiblast, repress Wnt activity with increasing strength. This leads to a graded repression of the Brachyury/T transcription factor, reducing mesoderm ingression and slowing down the elongation process. Due to the continuation of somite formation, the PSM, which is not fed with sufficient supply of new cells posteriorly, becomes progressively exhausted, ultimately leading to an arrest of segment formation. Our data provide a conceptual framework to explain how the cross-talk between the segmentation clock and the Hox clock accounts for the diversity of vertebral formulae across animal species. Primitive streak aera corresponding to PSM precursors were dissected in Stage 9 somites chicken embryo overexpressing HoxA13 or a control H2B-Venus. The experiment was designed to have biological duplicate in each conditions. The gain-of-function was obtained by electroporating the embryo at Stage 5HH with a vector containing HoxA13 under the CAGGS promoter with an H2B venus reporter. In order to have enough material for the microarray, 7 embryos were pooled in each sample before the hybridization.

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Bulk RNA-seq of PSCs and induced PSM cells from six different mammalian species

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