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Gene expression of Rif1-depleted ES cells

ABSTRACT: Gene expression of Rif1-depleted ES cells

PROVIDER: PRJNA664379 | ENA |

REPOSITORIES: ENA

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Gene expression of Rif1-depleted ES cells

Project description:Rif1 depletion in mouse ES cells increases the populations derepressing 2-cell zygote-specific genes including Zscan4. We investigated the chromatin structural change in the Zscan4 gene loci, and found that this region was deprived of major histone modifications except for moderately coded by H3 lysine9 trimethylation. Rif1 depletion caused no significant alteration in DNA methylation and histone modifications including common active marks, but only a notable increase in H3K27Ac active mark in gene bodies and neighboring regions, indicating that atypical broad enhancer-like chromatin with semi-silent property has been emerged in Zscan4 gene loci.<BR>In this study, we used microarrays to present the global changes in gene expression caused by transient depletion of Rif1.

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Project description:Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1. Methods: We performed global gene expression analysis of Rif1 knockdown ES cell lines using Affymetrix 430 2.0 arrays, compared to shRNA controls. J1 ES cells were transfected with Control shRNA and Rif1 shRNA using lipofectamine 2000. Forty-eight hours after transfection, cells were collected for global gene expression analysis using Affymetrix mouse genome 430 2.0 array. Stable F1 Rif1 knockdown ES cells at passage 16 were used for long-term gene expression chip microarray using Affymetrix mouse genome 430 2.0 array.

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Project description:RNAseq datasets from control and RIF1-depleted mouse embryos to address whether RIF1 depletion results in changes in gene expression. siRNA was microinjected at the zygote stage and controls (embryos injected with siRNA control) and RIF1-depleted embryos (embryos injected with siRNA against Rif1) were collected either at the 4-cell or at the 8-cell stage. RNAseq was performed using SMART-Seq2 in single embryos.

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