Expression Profiling of Term Placenta in Viviparous Mammals by RNA-Seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus Mus musculus Pan paniscus Canis lupus familiaris Monodelphis domestica Loxodonta africana Dasypus novemcinctus Ateles fusciceps
PROVIDER: GSE79121 | GEO | 2017/05/12
SECONDARY ACCESSION(S): PRJNA314981
REPOSITORIES: GEO
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Project description:The placenta is arguably the most anatomically variable organ in mammals. Understanding gene expression patterns among placentas from multiple species can illuminate the molecular basis of placenta function as well as potentially enrich our knowledge of the biology of obstetrical syndromes. We measured the expression profiles of the term placenta of multiple therian mammals using RNA-Seq. We identified multiple genes and transcripts which are differentially expressed across lineages including prolactin, relaxin, and galectins, as well as identifying the non-housekeeping genes which are core to placenta function (such as components of annexin complexes) in all species studied. RNAseq data from term placentas of 8 species with one sample per species
2017-05-12 | E-GEOD-79121 | biostudies-arrayexpress
Project description:Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.
2022-12-08 | GSE206075 | GEO
Project description:A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved or lost uterine expression during the origins of mammalian pregnancy, including the loss of genes responsible for the mineralization of the eggshell in the Mammalian and Therian stem-lineages, and the recruitment of genes into uterine expression that mediate maternal-fetal communication and maternal immunotolerance of the fetal allograft in the Therian and Eutherian stem-lineages. Our results indicate that one of the defining mammalian novelties evolved through a step-wise process that dramatically changed uterine gene expression, generating a suite of evolutionary innovations that support prolonged gestations. We report genome-wide gene expression generated by mRNA-Seq from the pregnant endometrium of dog, armadillo, and the platypus.
2015-01-30 | E-GEOD-57714 | biostudies-arrayexpress
Project description:<p>Therian mammals and angiosperms evolved genomic imprinting in nutritive tissues, the placenta and endosperm, where maternal and paternal genomes are in conflict with respect to resource allocation. In imprinted genes, transcription is repressed from either the paternal or the maternal allele, resulting in allele specific expression (ASE). We studied variation in ASE of imprinted genes in human placentas to detect loss of imprinting (LOI), which refers to departures from mono-allelic expression. The placental tissue was collected in connection with a multigenerational, prospective cohort study in Mali, West Africa, in which individuals were followed from infancy and early childhood to adulthood (age 18+ years). When young women for whom we had longitudinal growth data gave birth, we collected placental tissue and umbilical cord tissue. We genotyped the umbilical cord tissue and saliva samples from parents using targeted DNAseq to identify SNPs in 96 genes known from the literature to be imprinted in human placentas. We used RNAseq to analyze allele specific expression of the heterozygous SNPs. Our results provide the first systematic analysis of variation in LOI across genes and individuals and make it possible to test the hypothesis that modulation of imprinting is an epigenetic mechanism that contributes to the regulation of offspring growth. </p>
| phs001782 | dbGaP
Project description:Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylation domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. However, not all species have clear PMD/HMDs in their placentas. Instead what is conserved is higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification compared with the rest of the genome. As in human placenta, high gene body methylation is associated with higher gene expression across species. Analysis of DNA methylation in mouse and cow oocytes shows the same pattern of gene body methylation over many of the same genes as in the placenta, suggesting that this conserved pattern of active gene body methylation of the placenta may be established very early in development. MethylC-seq on placentas of 7 mammals, trophoblasts of rhesus, brains of 3 mammals, oocytes of cow, and human cordblood
2015-08-05 | E-GEOD-63330 | biostudies-arrayexpress
Project description:Annexin A3 (Anxa3) is a member of the calcium-regulated, cell membrane binding family of Annexin proteins. We previously confirmed that Anxa3 is expressed in the endothelial lineage in vertebrates and that loss of Anxa3 in Xenopus laevis leads to embryonic blood vessel defects. However, the biological function of Anxa3 in mammals is completely unknown. In order to investigate Anxa3 vascular function in mammals, we generated an endothelial cell specific Anxa3 conditional knockout mouse model (Anxa3f/f;Tie2-Cre).
2019-08-08 | GSE135528 | GEO
Project description:The relaxin-RXFP1 signaling loop promotes survival and proliferation in a panel of high-grade serous ovarian (HGSOC) cancer cell lines. Knockdown of either the relaxin receptor-1(RXFP1) or relaxin-2 (RLN2) decreased growth and tumorigenicity and increased apoptosis in dependent HGSOC cell lines. Transcriptome profiling of relaxin-dependent HGSOC cells using RNA-Seq revealed genes with altered expression levels following relaxin treatment. This included components of the Notch signaling pathway (NOTCH1 and NOTCH3), Wnt signaling (DVL1, LRP5, BCL9) and extracellular matrix regulation (VEGF-A, MMP9, MMP23). Collectively, genes and pathways upregulated by relaxin provide insight into the mechanisms by which it sustains proliferation of dependent cells.
2020-12-31 | GSE151280 | GEO
Project description:Background: ‘Healthy’ aging drives structural and functional changes in the heart including maladaptive electrical remodeling, fibrosis and inflammation, which lower the threshold for cardiovascular diseases such as heart failure (HF) and atrial fibrillation (AF). Despite mixed results in recent clinical trials, Relaxin-therapy for 2-days could reduce mortality by 37% at 180-days post-treatment, in patients with acute decompensated HF. Relaxin’s short life-span (hours) but long-lasting protective actions led us to test the hypothesis that relaxin acts at a genomic level to reverse maladaptive remodeling in aging and HF. Methods and Results: Young (9-month) and aged (24-month), male and female F-344/Brown Norway rats were treated with relaxin (0.4 mg/kg/day) for 2-weeks delivered by subcutaneous osmotic mini-pumps or with sodium acetate (controls). The genomic effects of aging and relaxin were evaluated by extracting RNA from the left ventricles and analyzing genomic changes by RNA-sequencing, Ingenuity Pathway Analysis, MetaCore and tissue immunohistochemistry. We found that aging promotes a native inflammatory response with distinct sex-differences and relaxin suppresses transcription of multiple genes and signaling pathways associated with inflammation and HF in both genders. In addition, aging significantly increased macrophage infiltration in the ventricles and activation of the complement cascade, and relaxin reversed these age-related effects. Conclusion: These data support the hypothesis that relaxin alters gene transcription and suppresses inflammatory pathways and genes associated with HF and aging. Relaxin’s suppression of inflammation and fibrosis supports its potential as a therapy for cardiovascular and inflammation-related diseases, such as HF, AF and diabetes.
2018-01-04 | GSE106377 | GEO
Project description:A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. We show that thousands of genes evolved or lost uterine expression during the origins of mammalian pregnancy, including the loss of genes responsible for the mineralization of the eggshell in the Mammalian and Therian stem-lineages, and the recruitment of genes into uterine expression that mediate maternal-fetal communication and maternal immunotolerance of the fetal allograft in the Therian and Eutherian stem-lineages. Our results indicate that one of the defining mammalian novelties evolved through a step-wise process that dramatically changed uterine gene expression, generating a suite of evolutionary innovations that support prolonged gestations.
2015-01-30 | GSE57714 | GEO
Project description:In eutherian mammals, dosage compensation of X-linked genes is achieved by X chromosome inactivation. X inactivation is random in embryonic and adult tissues, but imprinted X inactivation (paternal X silencing) has been identified in the extraembryonic membranes of the mouse, rat, and cow. Few other species have been studied for this trait, and the data from studies of the human placenta have been discordant or inconclusive. Here, we quantify X inactivation using RNA sequencing of placental tissue from reciprocal hybrids of horse and donkey (mule and hinny). In placental tissue from the equid hybrids and the horse parent the allelic expression pattern was consistent with random X inactivation, and imprinted X inactivation can clearly be excluded. We characterized horse and donkey XIST gene, and demonstrated that XIST allelic expression in female hybrid placental and fetal tissues is negatively correlated with the other X-linked genes chromosome-wide, which is consistent with the XIST-mediated mechanism of X inactivation discovered previously in mice. As the most structurally and morphologically diverse organ in mammals, the placenta also appears to show diverse mechanisms for dosage compensation that may result in differences in conceptus development across species. Examine allelic expression from individual samples of invasive trophoblast tissue of the chorionic girdle from gestation day 33-34 conceptuses of 5 horses, 3 donkeys, 6 mules, and 1 hinny.
2012-05-29 | E-GEOD-36352 | biostudies-arrayexpress