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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [RNA-seq]

ABSTRACT: ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted next generation sequencing of polyA-enriched bulk RNA in single and compound knockouts of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, and primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state.

ORGANISM(S): Homo sapiens

PROVIDER: GSE270786 | GEO | 2024/08/20

REPOSITORIES: GEO

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]

Project description:ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we conducted ATAC-seq in single and compound knockout of ZIC2, ZIC3 and ZIC5 primed hESCs, naïve hESCs lacking ZIC3 that inducibly express ZIC2, naive hESCs that inducible express ZIC2 or ZIC3, ZIC3-depleted primed hESCs that were cultured in 5iLAF medium for six days and undergoing reversion to a naive state, naive hESCs expressing ectopic ZIC2 in the presence of a BRG1 PROTAC.

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [CUT&Tag]

Project description:ZIC2 and ZIC3 are essential for acquisition and maintenance of primed pluripotency. In this study, we profiled chromatin occupancy of BRG1, EZH2, H3K27ac and H3K4me3 upon concomitant loss of ZIC2 and ZIC3 in primed hESCs, and of BRG1 upon ectopic expression of ZIC2 for increasing periods of time in naïve hESCs.

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq]

Project description:The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by strict epigenetic mechanisms. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 achieve their function by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to mesendoderm differentiation. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency

Project description:ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [CUT&Tag]

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]

Project description:ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]

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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [RNA-seq]

Project description:ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [RNA-seq]

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Zic2, an enhancer-binding factor required for embryonic stem cell specification

Project description:The Zinc finger protein of the cerebellum 2 (Zic2) is one of the vertebrate homologs of the Drosophila pair-rule gene odd-paired (opa). Our molecular and biochemical studies have demonstrated that Zic2 to preferentially bind to transcriptional enhancers and functions as a cofactor that interacts with the NuRD complex in ES cells. Detailed genome-wide studies demonstrate that Zic2 function with Mbd3/NuRD in regulating the chromatin state and transcriptional output of genes linked to differentiation. Zic2 is dispensable for the selfrenewal of ES cells but is required for proper differentiation, similar to what has been previously reported for Mbd3/NuRD. Our study identifies Zic2 as a key factor in the execution of the pluripotency program with Mbd3/NuRD in ES cells. ChIP-seq of Zic2, Chd4, Mbd3 and Zic3 in mES cells. ChIP-seq of H3K27me3, H3K27ac, H3K4me3, H3K4me1 and PolII in mES cells after Zic2 shRNA and non-targeting shRNA. RNA-seq of mES cells after Zic2, Zic3, Mbd3 and Mta2 shRNA and non-targeting shRNA.

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Identification of ZIC2 target genes in human pancreatic cancer cell lines PANC-1 and KP-4

Project description:PANC-1Tet/ZIC2 and PANC-1Tet/empty were established from human pancreatic cancer cell line PANC-1. PANC-1Tet/ZIC2 cells express FLAG-tagged human ZIC2 on the withdrawal of DOX. On the other hand, PANC-1Tet/empty was transfected an empty vector for the control experiment. To identify ZIC2 target genes, total RNAs were purified from the cells before and 48 hours after the DOX withdrawal. Gene expression profiles were analyzed by AGILENT human 4x44k cDNA microarray. As well as ZIC2-inducible system, we performed ZIC2-knockdown experiments in PANC-1 human pancreatic cancer cells. After 96 hours transfection of siRNAs for ZIC2 and its control, total RNAs were purified and gene expression profiles were analyzed by AGILENT human 4x44k cDNA microarray. ZIC2 target genes were identified in PANC-1 cells. Gene expression profiles of PANC-1Tet/ZIC2 and PANC-1Tet/empty cells were analyzed by AGILENT human 4x44k cDNA microarray before and 48 hours after the DOX withdrawal. As well as ZIC2-inducible system, gene expression profiles of control- and ZIC2-knocdown PANC-1 cells were also analyzed by AGILENT human 4x44k cDNA microarray.

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