Characterization and comparative analyses of transcriptomes of cloned and in vivo fertilized porcine pre-implantation embryos
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517319 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8492020_1.fastq.gz | Fastqsanger.gz | |||
| SRR8492020_2.fastq.gz | Fastqsanger.gz | |||
| SRR8492030_1.fastq.gz | Fastqsanger.gz | |||
| SRR8492030_2.fastq.gz | Fastqsanger.gz | |||
| SRR8492040_1.fastq.gz | Fastqsanger.gz |
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Project description:By using RNA-Seq technology, we get genome-wide transcriptome profiles of cloned and in vivo fertilized porcine embryos, from the oocyte to the blastocyst stages. We identified differentially expressed genes between the cloned and in vivo fertilized embryos from distinct stages of development and uncovered associated cellular signaling pathways and upstream transcription factors.
2019-04-29 | GSE125706 | GEO
Project description:Somatic cell nuclear transfer (SCNT) is the only method known to rapidly reprogram differentiated cells into totipotent embryos. Most cloned embryos become arrested before implantation and the details of the underlying molecular mechanism remain largely unknown. Dynamic regulation of the transcriptome is a key molecular mechanism driving early embryonic development. Here, we report comprehensive transcriptomic analysis of cloned embryos (from Laiwu and Duroc pigs) and in vivo fertilized embryos (from Duroc pigs) using RNA-sequencing. Comparisons between gene expression patterns were performed according to differentially expressed genes, specific-expressed genes, first-expressed genes, pluripotency genes and pathway enrichment analysis. In addition, we closely analyzed the improperly expressed histone lysine methyltransferases and histone lysine demethylases during cell reprogramming in cloned embryos. In summary, we identified altered gene expression profiles in porcine cloned pre-implantation embryos in comparison to normal in vivo embryos. Our findings provide a substantial framework for further discovery of the epigenetic reprogramming mechanisms in porcine SCNT embryos.
| S-EPMC6504007 | biostudies-literature
Project description:Comparison of gene expression in in vivo derived pre-implantation porcine embryos in order to define molecular mechanisms involved in embryo development. Keywords: parallel sample
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Project description:Comparison of gene expression in in vivo derived pre-implantation porcine embryos in order to define molecular mechanisms involved in embryo development. Keywords: parallel sample
2004-07-01 | E-GEOD-1453 | biostudies-arrayexpress
Project description:Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of embryo development and implantation in mammals via posttranscriptional gene regulation mechanisms. Applying custom made multispecies arrays we aimed to analyze expression profile of microRNAs in peri-implantation porcine conceptuses/trophoblasts to identify their potential role at the maternal-fetal interface during the critical period of maternal recognition of pregnancy and implantation.
2014-12-05 | GSE59618 | GEO
Project description:Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of embryo development and implantation in mammals via posttranscriptional gene regulation mechanisms. Applying custom made multispecies arrays we aimed to analyze expression profile of microRNAs in peri-implantation porcine conceptuses/trophoblasts to identify their potential role at the maternal-fetal interface during the critical period of maternal recognition of pregnancy and implantation. miRNA expression profiles were analyzed in samples collected from embryos or trophoblast on Days 10, 11, 12, 16 and 20 of pregnancy. Each group was represented by five to nine samples.
2014-12-05 | E-GEOD-59618 | biostudies-arrayexpress
Project description:Porcine somatic cell nuclear transfer (SCNT) is currently inefficient, as 1-3.95% of reconstructed embryos survive to term; inadequate or erroneous epigenetic reprogramming of the specialized donor somatic nucleus could be a primary reason. Therefore, a locus-specific analysis of DNA methylation dynamics in embryogenesis and the DNA methylation status of gametes and donor cells used for SCNT were conducted in the following developmentally important gene loci: POU5F1, NANOG, SOX2, H19, IGF2, IGF2R, XIST; and the retrotransposon LINE-1. There were significant epigenetic differences between the gametes and the somatic donor cells. Three gamete-specific differentially methylated regions (DMRs) in POU5F1, XIST, and LINE-1 were identified. A delayed demethylation process at POU5F1 and LINE-1 loci occurred after three successive cleavages, compared to the in vitro fertilized (IVF) embryos. Although cloned embryos could undergo de-methylation and re-methylation dynamics at the DMRs of imprinted genes (H19, IGF2R, and XIST), the re-methylation process was compromised, unlike in fertilized embryos. LINE-1 loci are widely dispersed across the whole genome, and LINE-1 DMR might be a potential porcine nuclear reprogramming epi-marker. Data from observations in our present and previous studies, and two published articles were pooled to produce a schematic diagram of locus-specific, DNA methylation dynamics of cloned and IVF embryos during porcine early embryogenesis. This also indicated aberrant DNA methylation reprogramming events, including inadequate DNA demethylation and insufficient re-methylation in cloned embryos. Further research should focus on mechanisms underlying demethylation during the early cleavage of embryos and de novo DNA methylation at the blastocyst stage.
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Project description:Although somatic cell nuclear transfer (SCNT) cloning is more efficient in cattle than in any 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 peri-implantation period. Therefore, we evaluated the response of the endometrium to SCNT embryos (produced from 7 different fetal fibroblast cell lines) as compared with embryos derived from in vitro fertilization (IVF). SCNT embryos and IVF embryos were cultured under identical conditions to the blastocyst stage (day 7) and were transferred to corresponding recipients, which were slaughtered at day 18 of pregnancy. The mRNA profiles of endometrium samples were obtained using a custom cDNA microarray enriched for transcripts differentially expressed in the endometrium and/or oviduct epithelium during the estrous cycle and/or early pregnancy. Overall, the variation in mRNA profiles was greater in the SCNT group than in the IVF group. Furthermore, 58 transcripts were differentially abundant in endometria from SCNT and IVF pregnancies. Prominent examples are orphan nuclear receptor COUP-TFII and connexin 43, both known to play important roles in uterine receptivity and conceptus placentation. These findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication that develops during the peri-implantation period. Endometrium transcriptome profiles may serve as a tool to evaluate SCNT embryos for their ability to establish pregnancy and develop a functional placenta.
| S-EPMC2666995 | biostudies-literature
Project description:Transcriptiome analysis is an excellent approach to understand the mechanism underlying nuclear reprogramming in somatic-cell-cloned embryos. Analysis of the transcriptomic data from the oocyte to blastocyst stage revealed that specific genes were inappropriately reprogrammed at each stage. Sertoli cell-cloned embryos appear to develop normally because the progression of incorrect reprogramming is concealed throughout development. The time-lapse gene expression profiles provide valuable information for understanding reprogramming in SCNT embryos. Single mouse oocyte (MII metaphase), in vitro fertilized embryo (replicates = 3 / each stage) and Sertoli cell cloned embryo (replicates = 5 / each stage) from 1-cell stage to blastocyst stage (16, 32, 48, 62, 72, 84 hours after sperm addition or activation) was used for total RNA extraction. Totally 51 Affymetrix microarrays were used in the experiment.
2013-04-05 | E-GEOD-41358 | biostudies-arrayexpress
Project description:To determine the effect of Zika virus infection on pre-implantation embryonic development, we performed single blastocyst RNA-Seq on MOCK and ZIKV infected embryos. ZIKV infection results in an increased risk of spontaneous abortion and poor intrauterine growth although the mechanisms underlying fetal loss remain undetermined. Little is known about the impact of ZIKV infection during the earliest stages of pregnancy, or pre- and peri-implantation, because most current studies of ZIKV infection in pregnancy models focus on post-implantation stages. Here, we demonstrate that trophectoderm cells of pre-implantation human and mouse embryos can be efficiently infected with ZIKV, and that trophectoderm can propagate virus causing cell death of neural progenitors. These findings were corroborated by our demonstration that hESC-derived trophectoderm cells are infected by ZIKV in a dose dependent manner. RNAseq of single blastocysts revealed key transcriptional changes in cellular and physiologic functions upon ZIKV infection, including nervous system development and function, prior to commitment to the neural cell lineage. Finally, the pregnancy rate of mice infected pre-implantation was > 50% lower than females infected at E4.5. These results demonstrate that pre-implantation ZIKV infection of trophectoderm leads to miscarriage or spontaneous abortion. Moreover, pre- and peri-implantation ZIKV infects trophectoderm cells that propagate virus over time causing cell death in neural progenitors. Cumulatively, these data demonstrate that vertical pre- and peri-implantation ZIKV infection of trophectoderm impairs fetal development and causes neural progenitor cell death, elucidating a previously unappreciated association of pre- and peri-implantation ZIKV infection and microcephaly.
2019-08-16 | GSE133254 | GEO