Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA308219 | ENA |
REPOSITORIES: ENA
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Project description:DNA Methylation Barcodes in Human Fetal Tissues and Human Induced Pluripotent Stem Cells
| PRJNA308218 | ENA
Project description:DNA Methylation Barcodes in Human Fetal Tissues and Human Induced Pluripotent Stem Cells I
| PRJNA308220 | ENA
Project description:DNA methylation is essential for mammalian development. Studies of the catalytically inactive DNA methyltransferase Dnmt3l have mainly been limited to mice where Dnmt3l was shown to be essential for fertility, de novo DNA methylation in early embryos and maintenance of DNA methylation patterns in mouse pluripotent stem cells. Recent work revealed that DNMT3L is the most highly enriched chromatin factor in naive human pluripotent stem cells (hPSCs) compared with primed hPSCs. Stem cell-based human embryo models and naive hPSCs provide a unique opportunity to functionally dissect human developmental mechanisms. Here we use naive hPSCs and human blastoids, a 3D human blastocyst model, to investigate the functional impact of DNMT3L on human naive pluripotency and preimplantation development. We demonstrate an essential role of DNMT3L in trophectoderm cell fate induction, maintenance of DNA methylation patterns and chromatin states in naive hPSCs, and blastoid lineage identity. We further show that DNMT3L promotes reprogramming to naive pluripotency, and has integrated a hominoid-specific naive human pluripotency gene regulatory program involving evolutionary recent transposable elements. Therefore, DNMT3L plays conserved and hominoid-specific functions in human naive pluripotency and pre-implantation development.
2026-08-25 | PXD055233 | Pride
Project description:DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time
| PRJNA132363 | ENA
Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 21 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 6 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 7 control embryonic stem cell (ESC) lines.
2014-11-06 | E-GEOD-61461 | biostudies-arrayexpress
Project description:Transcription factor-mediated reprogramming yields induced pluripotent stem cells (iPSC) by erasing tissue specific methylation and re-setting DNA methylation status to an embryonic stage. We compared bona fide human iPSC derived from umbilical cord blood (CB) and neonatal keratinocytes (K). Through both incomplete erasure of tissue specific methylation and de novo tissue specific methylation, CB-iPSC and K-iPSC are distinct in genome-wide DNA methylation profiles. Functionally, CB-iPSC displayed better blood formation in vitro, whereas K-iPSC differentiated better to a keratinocyte fate, implying that the tissue of origin needs to be considered in future therapeutic applications of human iPSCs. We performed gene expression and global DNA methylation profiling on iPS and the source somatic cell types to search for evidence of epigenetic memory. We performed gene expression profiling to identify genes differentially expressed between keratinocytes and cord blood, and from induced pluripotent stem cells from these somatic tissues.
2011-11-29 | E-GEOD-27186 | biostudies-arrayexpress
Project description:Genome-wide analysis of histone modification (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3), protein-DNA binding (TAF1, P300, Pou5f1 and Nanog), cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells We generated histone modification data (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3) and protein-DNA binding data (TAF1, P300, Pou5f1 and Nanog) using Chromatin Immunoprecipitation followed by short sequencing (ChIP-seq), cytosine methylation data using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq), transcriptome data with RNA short sequencing (RNA-seq) in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation. Examination of 8 histone modifications, 4 protein-DNA binding, cytosine methylation and transcriptome in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation.
2012-02-28 | E-GEOD-36114 | biostudies-arrayexpress
Project description:Studies of the catalytically inactive DNA methyltransferase Dnmt3l have mainly been limited to mice where Dnmt3l was shown to be essential for fertility, de novo DNA methylation in early embryos and maintenance of DNA methylation patterns in mouse pluripotent stem cells. In humans, recent work revealed that DNMT3L is the most highly enriched chromatin factor in naive pluripotent stem cells (hPSCs) compared with primed hPSCs. Naive hPSCs and stem cell-based human embryo models provide a unique opportunity to functionally the role of DNMT3L in human naive pluripotency and development. Here we use naive hPSCs and human blastoids, 3D blastocyst models, to investigate the functional impact of DNMT3L on human naive pluripotency and preimplantation development. We demonstrate an essential role of DNMT3L in maintenance of DNA methylation patterns and chromatin states in naive hPSCs, and in trophectoderm cell fate induction and blastoid lineage identity. We further show that DNMT3L promotes reprogramming to naive pluripotency, and has integrated a hominoid-specific naive human pluripotency gene regulatory program involving evolutionarily recent transposable elements. Our work provides crucial insights into the molecular basis of human naive pluripotency and sheds light on human preimplantation development.
2026-08-31 | PXD053638 | Pride
Project description:Comparison of DNA methylation in CRISPRa induced human pluripotent stem cell lines, control iPSC line induced with Sendai viral vectors, H9 embryonic stem cell line and human foreskin fibroblasts.
2018-06-07 | E-MTAB-6194 | biostudies-arrayexpress
Project description:Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [Undifferentiated human induced pluripotent stem cells]
| PRJNA259832 | ENA