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Chromatin structure programs between genetically matched PEF and porcine iPSCs

ABSTRACT: Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.

ORGANISM(S): Sus scrofa

PROVIDER: GSE173275 | GEO | 2022/10/19

REPOSITORIES: GEO

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Gene expression programs between genetically matched PEF and porcine iPSCs

Project description:Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.

2022-10-19 | GSE173304 | GEO

ESRRB Facilitates the Conversion of Trophoblast-like Stem Cells from Induced Pluripotent Stem cells by Directly Regulating KRT8 and CDX2

Project description:Porcine induced pluripotent stem cells (piPSCs) could serve as a great model system for human stem cell pre-clinical research. However, the pluripotency gene network of piPSCs, especially the function for the core transcription factor ESRRB, was poorly understood. Here, we constructed ESRRB-overexpressing piPSCs (ESRRB-piPSCs). Compared with the control piPSCs (CON-piPSCs), the ESRRB-piPSCs showed flat, monolayered colony morphology. Moreover, the ESRRB-piPSCs showed greater chimeric capacity into trophectoderm than CON-piPSCs. We found that ESRRB could directly regulate the expressions of trophoblast stem cell (TSC)-specific markers, including KRT8, KRT18 and CDX2, through binding to their promoter regions. Mutational analysis proved that the N-terminus zinc finger domain is indispensable for ESRRB to regulate the TSC markers. Furthermore, this regulation needs the participation of OCT4. Accordingly, the cooperation between ESRRB and OCT4 facilitates the conversion from pluripotent state to the trophoblast-like state.

2022-02-17 | PXD027539 | Pride

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LIN28A inhibited DUSP family phosphatases and activated MAPK signaling pathway to maintain pluripotency in porcine induced pluripotent stem cells

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ESRRB facilitates the conversion of Trophoblast-like Stem Cells from induced pluripotent stem cells by directly regulating KRT8 and CDX2 [RNA-seq]

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2021-10-14 | GSE180057 | GEO

ESRRB facilitates the conversion of Trophoblast-like Stem Cells from induced pluripotent stem cells by directly regulating KRT8 and CDX2 [ChIP-seq]

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Identification of chromatin accessibility during the early stage of pig SCNT embryo reprogramming by ATAC-seq

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2023-11-16 | GSE161563 | GEO

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