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Discovery of novel imprinted genes by transcriptional analysis of parthenogenetic embryonic stem cells

ABSTRACT: Parthenogenetic embryonic stem cells (PESCs) may have future utility in cell replacement therapies. We examined genome-wide mRNA expression profiles of monkey PESCs relative to ESCs derived from fertilized embryos. Several known paternally-imprinted genes were in the highly down-regulated group in PESCs compared to ESCs. Allele specific expression analysis of paternally-imprinted genes, i.e., those genes whose expression is down-regulated in PESCs, led to the identification of one novel candidate that was exclusively expressed from a paternal allele. Our findings suggest that PESCs could be used as a model for studying genomic imprinting and in the discovery of novel imprinted genes. Keywords: gene expression

ORGANISM(S): Macaca mulatta

PROVIDER: GSE17964 | GEO | 2010/06/21

SECONDARY ACCESSION(S): PRJNA119933

REPOSITORIES: GEO

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Discovery of novel imprinted genes by transcriptional analysis of parthenogenetic embryonic stem cells

Project description:Parthenogenetic embryonic stem cells (PESCs) may have future utility in cell replacement therapies. We examined genome-wide mRNA expression profiles of monkey PESCs relative to ESCs derived from fertilized embryos. Several known paternally-imprinted genes were in the highly down-regulated group in PESCs compared to ESCs. Allele specific expression analysis of paternally-imprinted genes, i.e., those genes whose expression is down-regulated in PESCs, led to the identification of one novel candidate that was exclusively expressed from a paternal allele. Our findings suggest that PESCs could be used as a model for studying genomic imprinting and in the discovery of novel imprinted genes. Keywords: gene expression The transcriptomes of rhesus monkey embryonic stem cell lines derived from IVF-produced embryos (Oregon Rhesus Macaque Embryonic Stem, ORMES-22) were compared with rhesus monkey parthenogenetic embryonic stem cell lines (heterozygous rhesus Parthenogenetic embryonic stem cell lines, rPESC-2) and homozygous rhesus Parthenogenetic embryonic stem cell lines, ORMES-9). Moreover, the transcriptomes of rPESC-2 line were also compared with ORMES-9. Finally, the adult somatic skin fibroblasts were analyzed. Three biological replicates of each cell line (A, B, C) were analyzed.

2010-07-07 | E-GEOD-17964 | biostudies-arrayexpress

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2013-04-04 | E-GEOD-45749 | biostudies-arrayexpress

mRNA expression profiles in androgenetic, parthenogenetic and fertilized embryonic stem cells

2013-04-04 | GSE45749 | GEO

Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [microarray]

Project description:Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here we explored molecular and developmental aspects of imprinting in humans by generating exclusively-paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively-maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent-cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered new imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a novel bias towards liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

2019-09-05 | GSE114676 | GEO

Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq I]

Project description:Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here, we explored molecular and developmental aspects of imprinting in humans by generating exclusively paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs, and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a similar bias toward liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

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Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq II]

Project description:Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here, we explored molecular and developmental aspects of imprinting in humans by generating exclusively paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs, and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a similar bias toward liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

2019-09-05 | GSE114677 | GEO

mRNA expression data from human parthenogenetic haploid ESCs (hPGES), normal ESCs (H9) and human fibroblast

Project description:Here we report the derivation of human haploid ESCs from parthenogenetic haploid embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES), normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.

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microRNA expression profiles in androgenetic, parthenogenetically activated and fertilized embryonic stem cells

2013-04-04 | GSE45753 | GEO

microRNA expression profiles in androgenetic, parthenogenetically activated and fertilized embryonic stem cells

Project description:In this study, miRNA expression profiles were examined by Illumina microarray in mouse embryonic stem cells (ESCs) derived from androgenetic (aESC), parthenogenetic (pESC) and fertilized (fESC) blastocysts. Results showed that 125, 42 and 99 miRNAs were differentially expressed in the aESCs vs. fESCs, pESCs vs. fESCs and aESCs vs. pESCs, respectively. Androgenetic, parthenogenetically activated and fertilized embryonic stem cell lines were established from androgenetic and fertilized blasotocyst. microRNA microarrays were repeated three times using passages 6, 7 and 8.

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Amplification of Oocytes through Parthenogenesis

Project description:We asked whether oocyte number could be amplified through parthenogenesis of mouse oocytes, without requiring creation of a paternal genome and a genetically unique genome. Parthenotes develop to a blastocyst-like stage, and from this parthenogenetic ESCs (pESCs) can be derived with high efficiency. Like ESCs, pESCs maintain unlimited self-renewal and pluripotency, as well as germline competence. Further, we demonstrate that their expression pattern of imprinted maternal genes resembles that observed in oocytes. pESCs can be directed to differentiate into primordial germ cell-like cells (PGCLCs) and form oocytes that produce fertile pups and reconstitute ovarian endocrine functions. The transcriptome and imprinting pattern of PGCLCs differentiated from pESCs more closely approximate those of in vivo produced embryonic PGCs, than PGCLCs produced from ESCs. Parthenogenesis offers a promising route for deriving PGCLCs and amplifying oocytes by faithfully maintaining maternal genes, without fertilization.

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