Single cell RNA-seq study of wild type and Hox mutant developing uterus
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PROVIDER: PRJNA484769 | ENA |
REPOSITORIES: ENA
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Project description:This study identifies a novel role for the Hoxc9,10,11 genes in uterine gland formation. This function is redundant with the Hoxa9,10,11 and Hoxd9,10,11 genes and is only seen in a sensitized genotype with reduced expression of these paralogs. We further used scRNA-seq to define the gene expression patterns of the multiple cell types of the developing uterus. The results define the gene expression patterns driving lineage specific development. In addition scRNA-seq was used to characterize the perturbed gene expression levels of all developing uterus cell types in the ACD+/- and ACD+/-WTA11 mutants. Particularly striking was the reduced Wnt signaling and the disruption of the Cxcl12/Cxcr4 axis in the mutants.
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Project description:The Hox complex consists of 39 genes arranged in 4 clusters of flanking genes and 13 paralogous groups in mammals. To assess the functional redundancy of Hox abdominal-B genes during renal development, we used a modified recombineering strategy to simultaneous introduce frameshift mutations into the Hox9, Hox10, and Hox11 flanking genes of the HoxA, HoxC, and HoxD paralogous groups. We performed RNA seq on whole kidneys at E18.5 in triplicates for representative genotypes including: wild type; Hoxa9,10,11-/- HoxC9,10,11+/-, Hoxa9,10,11+/- HoxC9,10,11-/-, Hoxa9,10,11-/- HoxC9,10,11-/-. Our results suggest that the loss of Hox function results in a partial metanephric to mesonephric transformation, with tubules co-expressing markers of both proximal tubules and collecting ducts, as well as markers of mesonephric-derived epididymis tubules.
2018-04-25 | GSE90816 | GEO
Project description:Epithelial gland development within the uterine lining during prepubertal period is important to ensure successful gestation in adults. Lgr5 expression in uterus becomes largely restricted to the tips of developing glands after birth. These Lgr5 highly expressing cells function as stem cells during gland development. We used microarrays to detail the gene expression profilings and compare between Lgr5 highly and negatively expressing cells in developing uterus.
2019-09-26 | GSE137974 | GEO
Project description:Geminin is required for Hox gene regulation to pattern the developing limb
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Project description:Background: Preterm birth is the leading cause of all infant mortality. In 2004, 12.5% of all births were preterm. In order to understand preterm labor, we must first understand normal labor. Since many of the myometrial changes that occur during pregnancy are similar in mice and humans and mouse gestation is short, we have studied the uterine genes that change in the mouse during pregnancy. Here, we used microarray analysis to identify uterine genes in the gravid mouse that are differentially regulated in the cyclooxygenase-1 knockout mouse model of delayed parturition. Methods: Gestational d18.0 uteri (n=4) were collected from pregnant wild-type and cyclooxygenase-1 knockout mice. Part of the uterus was used for frozen sections and RNA was isolated from the remainder. Microarray analysis was performed at the Indiana University School of Medicine Genomic Core and analyzed using the Microarray Data Portal. Northern analysis was performed to confirm microarray data and the genes localized in the gravid uterus by in situ hybridization. Results: We identified 277 genes that are abnormally expressed in the gravid d18.0 cyclooxygenase-1 knockout mouse. Nine of these genes are also regulated in the normal murine uterus during the last half of gestation. Many of these genes are involved in the immune response, consistent with an important role of the immune system in parturition. Expression of 4 of these genes; arginase I, IgJ, Tnfrsf9 and troponin; was confirmed by Northern analysis to be mis-regulated during pregnancy in the knockout mouse. In situ hybridization of these genes demonstrated a similar location in the gravid wild-type and Cox-1 knockout mouse uteri. Conclusions: To our knowledge, this is the first work to demonstrate the uterine location of these 4 genes in the mouse during late pregnancy. There are several putative transcription factor binding sites that are shared by many of the 9 genes identified here including; estrogen and progesterone response elements and Ets binding sites. In summary, this work identifies 9 uterine murine genes that may play a role in parturition. The function of these genes is consistent with an important role of the immune system in parturition. Experiment Overall Design: Gestational d18.0 uteri (n=4) were collected from pregnant wild-type and cyclooxygenase-1 knockout mice. Part of the uterus was used for frozen sections and RNA was isolated from the remainder. Microarray analysis (affymetrix 430 2.0) was performed at the Indiana University School of Medicine Genomic Core and analyzed using the Microarray Data Portal. In order to reduce the number of candidate parturition-related genes identified we compared the genes identified as abnormally expressed in the Cox-1 KO uterus to the genes that we had previously identified as changing from gestational d13.5 to d19.0 in the wild-type mouse uterus. Northern analysis was performed to confirm microarray data and the genes localized in the gravid uterus by in situ hybridization.
2008-06-16 | E-GEOD-8269 | biostudies-arrayexpress
Project description:Forkhead box A2 (FOXA2) is a critical regulator of endometrial gland development in mice. In the adult mouse uterus, FOXA2 is expressed solely in the GE cells of the endometrium. Conditional deletion of Foxa2 after birth in the uterus, using the progesterone receptor Cre mouse (PgrCre), impeded gland development, thereby rendering the adult mouse infertile due to defects in blastocyst implantation stemming from a lack of endometrial glands and their secretions. As a first step to begin understanding the FOXA2 function in the endometrial glands of the uterus, genome-wide investigation of in vivo FOXA2 and RNA polymerase II (POL2) binding target regions in the neonatal and adult uterus was determined by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq). In order to determine the transcriptional regulatory networks mediating FOXA2 regulation of endometrial gland development and function, chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) was used to create a genome-wide profile of in vivo FOXA2-binding sites in the developing (PD 12) and adult (DOPP 2.5 and 3.5) mouse uterus.
2013-12-01 | E-GEOD-48238 | biostudies-arrayexpress
Project description:Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5’ Hox transcription factor expression is essential for proper limb bud patterning and development. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5’ Hox gene expression expanded into more proximal and anterior regions of embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior Shh signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the Hoxd13 target Shh, and the Shh target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of Gli3, a Shh pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.
2020-06-05 | GSE143211 | GEO
Project description:Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.
2016-02-19 | GSE74692 | GEO