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Comprehensive role of Zfp217 in m6A methylation [ChIP-seq]

ABSTRACT: Many transcriptional and epigenetic networks must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming. Here, we explore the role of Zfp217 as a key transcriptional factor in maintaining ES cell self-renewal by permorming genome-wide ChIP-Seq analyses. Examination of Zfp217 binding profiling by high throughput sequencing in mouse stem cells

ORGANISM(S): Mus musculus

SUBMITTER: Martin Walsh

PROVIDER: E-GEOD-65730 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comprehensive role of Zfp217 in m6A methylation [MeRIP-seq]

Project description:Many transcriptional and epigenetic networks must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming. Here, we explore the role of Zfp217 as a key transcriptional factor in maintaining ES cell self-renewal by performing meRIP analysis in control and Zfp217-depleted mouse stem cells. Examination of m6A levels from total RNA in control and Zfp217 shRNA infected mouse stem cells

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Comprehensive role of Zfp217 in m6A methylation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Project description:The embryonic stem (ES) cell transcriptional and epigenetic networks are critical for the maintenance of ES cell self-renewal. However, it remains unclear whether components of these networks functionally interact and if so, what factors mediate such interactions. Here we show that WD-repeat protein-5 (Wdr5), a core member of the mammalian Trithorax (trxG) complex, positively correlates with the undifferentiated state and is a novel regulator of ES cell self-renewal. We demonstrate that Wdr5, an ‘effector’ of H3K4 methylation, interacts with the pluripotency transcription factor Oct4. In concordance, genome-wide ChIP-Seq and transcriptome analyses demonstrate overlapping gene regulatory functions between Oct4 and Wdr5. We show that the Oct4-Sox2-Nanog circuitry cooperates with trxG for transcriptional activation of key self-renewal regulators. Furthermore, Wdr5 expression is required for the efficient formation of induced pluripotent stem (iPS) cells. Collectively, these findings implicate an integrated model of transcriptional and epigenetic control, mediated by select trxG members, for the maintenance of ES cell self-renewal and somatic cell reprogramming. 7 Samples

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Comprehensive role of Zfp217 in m6A methylation [MeRIP-seq]

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Comprehensive role of Zfp217 in m6A methylation [ChIP-seq]

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Graded Nodal/Activin Signaling Governs ES Cell Fate Decisions via Differential Recruitment of Phospho-Smad2 to Oct4 and Distinct Target Gene Subsets.

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Project description:MicroRNAs (miRNAs) are crucial for normal embryonic stem (ES) cell self-renewal and cellular differentiation, but how miRNA gene expression is controlled by the key transcriptional regulators of ES cells has not been established. We describe here a new map of the transcriptional regulatory circuitry of ES cells that incorporates both protein-coding and miRNA genes, and which is based on high-resolution ChIP-seq data, systematic identification of miRNA promoters, and quantitative sequencing of short transcripts in multiple cell types. We find that the key ES cell transcription factors are associated with promoters for most miRNAs that are preferentially expressed in ES cells and with promoters for a set of silent miRNA genes. This silent set of miRNA genes is co-occupied by Polycomb Group proteins in ES cells and expressed in a tissue-specific fashion in differentiated cells. These data reveal how key ES cell transcription factors promote the miRNA expression program that contributes to self-renewal and cellular differentiation, and integrate miRNAs and their targets into an expanded model of the regulatory circuitry controlling ES cell identity. Keywords: ChIP-seq analysis of ES cell transcriptional regulators and chromatin modifications. Cell-type comparison of short RNA transcritome. Analysis of changes in short RNA transcritome upon Oct4 ablation. ChIP-seq in murine embryonic stem cells for Oct4, Sox2 (2 runs), Nanog (2 runs), Tcf3 (2 runs), Suz12 (2 runs), H3K4me3 (4 runs), H3k79me2 (2 runs), H3k36me3 (2 runs) and whole cell extract input DNA (WCE, 2 runs). Short transcript sequencing from murine embryonic stem cells (mES, v6.5), mouse embryonic fibroblasts (MEF), murine neural precursor cells (NPC), and ZHBT-c4 cells (from Austin Smith) untreated (0h), with 12 hours of doxycyclin treatment (12h), and with 24 hours of doxycyclin treatment (24h).

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