Amniogenesis occurs in two independent waves in primate embryos
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA743135 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15017783.fastq.gz | Fastqsanger.gz | |||
| SRR15017784.fastq.gz | Fastqsanger.gz | |||
| SRR15017785_1.fastq.gz | Fastqsanger.gz | |||
| SRR15017785_2.fastq.gz | Fastqsanger.gz | |||
| SRR15017786_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:In primates the amnion emerges through cavitation of the epiblast during implantation, whereas in other species by folding of the ectoderm later around gastrulation. How the mechanisms of amniogenesis diversified in evolution remains unknown. Here we employed the naïve-to-primed transition of human pluripotent stem cells (hPSC) to model peri-implantation epiblast development. We discovered that during this transition hPSC transiently gain the ability to differentiate into cavitating epithelium that transcriptionally matches the early amnion of human embryos. In contrast, primed hPSC produce cells resembling late amnion, uncovering an independent differentiation route. Unexpectedly, single-cell analysis of primate embryos revealed two transcriptionally distinct amniogenesis waves. The early wave occurs through a trophectoderm-like route and encompasses cavitation, whereas the late wave follows an ectoderm-like pathway during gastrulation. The discovery of two independent waves of amniogenesis both of which can be modelled in hPSC explains how amniogenesis through cavitation emerged during the evolution of primates.
2022-04-20 | GSE179309 | GEO
Project description:In primates, the amnion emerges through cavitation of the epiblast during implantation, whereas in other species it does so later at gastrulation by the folding of the ectoderm. How the mechanisms of amniogenesis diversified during evolution remains unknown. Unexpectedly, single-cell analysis of primate embryos uncovered two transcriptionally and temporally distinct amniogenesis waves. To study this, we employed the naive-to-primed transition of human pluripotent stem cells (hPSCs) to model peri-implantation epiblast development. Partially primed hPSCs transiently gained the ability to differentiate into cavitating epithelium that transcriptionally and morphologically matched the early amnion, whereas fully primed hPSCs produced cells resembling the late amnion instead, thus recapitulating the two independent differentiation waves. The early wave follows a trophectoderm-like pathway and encompasses cavitation, whereas the late wave resembles an ectoderm-like route during gastrulation. The discovery of two independent waves explains how amniogenesis through cavitation could emerge during evolution via duplication of the pre-existing trophectoderm program.
| S-EPMC9627701 | biostudies-literature
Project description:Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.
2025-08-27 | GSE305241 | GEO
Project description:Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar gene expression patterns and traits across lineages. However the mutational mechanisms driving these duplications and the regulatory changes enabling novel expression patterns remain poorly understood. The primate amylase locus, marked by independent gene duplications, provides an ideal model to investigate these dynamics. Leveraging high-quality genome assemblies from 53 primates and multi-tissue transcriptomes from Old World monkeys, we reconstructed the evolutionary history of the recurrent gene duplications across the primate phylogeny. Our data suggest that lineage-specific LTR retrotransposon insertions are associated with initial structural instability, while subsequent duplications are primarily driven by non-allelic homologous recombination. Recurrent independent duplications in rhesus macaques, olive baboons, and great apes gave rise to distinct amylase gene copies with convergent expression in the pancreas and salivary glands. We found that these independent gene duplications are accompanied by episodic diversifying selection on lineage-specific copies, likely driving the emergence of functional divergence. Our comparative analyses in primates indicate that the gene ancestral to great ape AMY1 and AMY2A was expressed in both salivary glands and pancreas in the Catarrhini ancestor. The great ape–specific duplication of this ancestral gene likely facilitated subfunctionalization into salivary gland- and pancreas-specific expression, respectively. Comparative analysis of primate amylase promoter regions reveals regulatory rewiring, driven by motif turnover mediated by structural rearrangements, and partially explaining evolutionary shifts in expression. Together, our findings highlight how structural and regulatory modularity in complex genomic regions drives evolutionary innovation and molecular convergence, and we provide a genomic framework for dissecting these processes across diverse lineages.
2025-08-27 | GSE305255 | GEO
Project description:Convergent evolution through independent rearrangements in the primate amylase locus [Baboon]
| PRJNA1304902 | ENA
Project description:Convergent evolution through independent rearrangements in the primate amylase locus [Rhesus]
| PRJNA1304929 | ENA
Project description:Development and tissue maintenance require a supply of new cells, which are generated by division of stem cells and then specialised to perform their function. The differentiation process requires the tight control of gene expression, but this has been challenging to study in a systematic manner in adult stem cells, which are sparsely distributed in tissues. We have overcome these limitations by establishing a robust protocol to synchronise Drosophila female germline stem cell (GSC) differentiation in vivo, allowing us to perform transcriptome and translatome analyses at high temporal resolution during differentiation. As well as observing dynamic changes in mRNA level, promoter usage and exon inclusion, our data reveal that changing translation efficiency is the predominant regulatory mechanism during GSC differentiation. Indeed, changes in mRNA level are frequently buffered by changes in translation efficiency, including the translational repression of transcripts that will only be translated later during oocyte maturation or embryo development. Contrary to the expected linear accumulation of changes from stem cell to differentiated cell, our data reveal that differentiation occurs through two distinct waves of changes in both the transcriptome and translatome level.
2024-02-21 | GSE246393 | GEO