Bovine PRD-like homeobox genes
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB70908 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:ETCHbox genes are mammalian-specific PRD class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. We ectopically expressed bovine ARGFX and LEUTX ETCHbox genes, both tagged with 3xFLAG tags, in bovine foetal fibroblasts and completed transcriptome seqencing. We compared the transcriptome of cells with ARGFX or LEUTX ectopic expression with control transfected cells. For ARGFX, we expressed the WT version of the gene and a mutant allele containing a 13bp frameshift deletion.
2022-05-24 | GSE192356 | GEO
Project description:PRD class homeobox genes in bovine early embryos: function, evolution and overlapping roles
| PRJNA791233 | ENA
Project description:In vitro maturation (IVM) of the oocytes is a routine method in bovine embryo production. The competence of bovine oocytes to develop into embryo after IVM and in vitro fertilization (IVF) is lower as compared to in vivo preovulatory oocytes. Cumulus cells (CC) that enclose an oocyte are involved in the acquisition of oocyte quality during maturation. Using transcriptomic approach we compared cumulus cells gene expression during IVM with that in vivo preovulatory period.
2011-08-09 | GSE31261 | GEO
Project description:Global hypermethylations of histone H3 lysine 9 (H3K9) tri- and di-methylation (H3K9me3/2) have been identified in bovine cloned embryos at the embryonic genome activation (EGA) stage (eight-cell stage), but the intrinsic reason for these anomalies remains elusive. To ascertain key factors responsible for aberrant H3K9 methylation, we performed RNA sequencing of transcripts in eight-cell bovine in vitro fertilized (IVF) and SCNT embryo. From the differentially expressed genes (DEGs) between IVF and SCNT embryos, we identified that the unsuccessful reactivation of two histone demethylases, KDM4D and KDM4E, is responsible for the incomplete H3K9me3/2 demethylation in SCNT embryos at the EGA stage. By mRNA injection, ectopic expression of either KDM4D or KDM4E could erase H3K9me3/2 barriers, improve blastocyst formation, and elevate cloning efficiency of bovine SCNT. To examine the detailed genes responsive to KDM4E overexpression, we also performed RNA sequencing of bovine eight-cell SCNT embryos with KDM4E compensation and found an obvious restoration of global transcriptional patterns in SCNT embryos. Our study first provides the transcriptome data set of bovine IVF and SCNT embryos during EGA with or without KDM4E overexpression, which advance the understanding of incomplete nuclear reprogramming, and contribute to the practical implications for genetically modified livestock breeding using SCNT.
2018-01-16 | GSE99294 | GEO
Project description:Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology RNA was extracted from individual D7 bovine blastocysts (Arcturus Picopure), cDNA was synthesized and amplified (Nugen Ovation) and indexed libraries were created for sequencing (Nugen Encore)
2013-02-03 | E-GEOD-44023 | biostudies-arrayexpress
Project description:Eutherian Totipotent Cell Homeobox (ETCHbox) genes are mammalian-specific PRD-class homeobox genes with conserved expression in the preimplantation embryo but fast-evolving and highly divergent sequences. Here, we exploit an ectopic expression approach to examine the role of bovine ETCHbox genes and show that ARGFX and LEUTX homeodomain proteins upregulate genes normally expressed in the blastocyst; the identities of the regulated genes suggest that, in vivo, the ETCHbox genes play a role in coordinating the physical formation of the blastocyst structure. Both genes also downregulate genes expressed earlier during development and genes associated with an undifferentiated cell state, possibly via the JAK/STAT pathway. We find evidence that bovine ARGFX and LEUTX have overlapping functions, in contrast to their antagonistic roles in humans. Finally, we characterize a mutant bovine ARGFX allele which eliminates the homeodomain and show that homozygous mutants are viable. These data support the hypothesis of functional overlap between ETCHbox genes within a species, roles for ETCHbox genes in blastocyst formation and the change of their functions over evolutionary time.
| S-EPMC9117796 | biostudies-literature
Project description:In vitro maturation (IVM) of the oocytes is a routine method in bovine embryo production. The competence of bovine oocytes to develop into embryo after IVM and in vitro fertilization (IVF) is lower as compared to in vivo preovulatory oocytes. Cumulus cells (CC) that enclose an oocyte are involved in the acquisition of oocyte quality during maturation. Using transcriptomic approach we compared cumulus cells gene expression during IVM with that in vivo preovulatory period. Global transcriptional profiling was performed using cumulus cells collected from mature bovine oocytes (metaphase-II stage) after maturation performed either in vivo or in vitro. In vivo matured cumulus cells were collected from ovulatory follicles of Montbeliard adult cows by ovum pick-up in vivo (OPU, n=4). In vitro matured cumulus cells were recovered from the oocytes after 22h of in vitro culture of cumulus-oocyte complexes (50 COC per experiment) from 2-6 mm ovarian follicles of adult cows (MIV, n=4). Gene expression analysis was carried out between in vivo and in vitro matured cumulus representing a total of 8 slides (dye swap protocol)
2011-08-08 | E-GEOD-31261 | biostudies-arrayexpress
Project description:Although somatic cell nuclear transfer (SCNT) cloning is more efficient in bovine than in all other species tested so far, there is a high rate of pregnancy failure that has been linked to structural and functional abnormalities of the placenta. We tested the hypothesis that these changes may originate from disturbed embryo-maternal interactions in the pre-implantation period. Therefore, we evaluated the transcriptome response of the endometrium to SCNT embryos (produced from five different donor cell cultures) as compared to embryos derived from in vitro fertilization (IVF). SCNT embryos and IVF embryos were cultured under identical conditions to the blastocyst stage (Day 8) and transferred to recipients. The recipients were slaughtered at day 18 of pregnancy and the uterus was recovered. Pregnancy was verified by the presence of at least one normally developed embryo. Transcriptome profiling of endometrium samples using a custom cDNA microarray covering transcripts expressed in the endometrium and/or oviduct epithelium revealed 58 transcripts that were differently abundant between endometrium samples from SCNT vs. IVF pregnancies. Prominent examples are NR2F2 (encoding the orphan nuclear receptor COUP-TFII) and GJA1 (encoding connexin 43). Both transcripts are known to play important roles in placentation and were significantly less abundant in endometrium from SCNT vs. IVF pregnancies. These findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication already in the pre- or peri-implantation period. Endometrium transcriptome profiles may serve as a novel readout to evaluate SCNT embryos for their ability to induce pregnancy with a functional placenta. Keywords: response to different embryos
2009-03-13 | GSE13663 | GEO
Project description:Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology
2013-02-03 | GSE44023 | GEO
Project description:Transcriptomes of bovine IVF embryos showing distinct developmental statuses were sequenced
2010-12-23 | GSE25082 | GEO