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Identification of candidate genes regulated by E4bp4 in murine bone marrow

ABSTRACT: E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP

ORGANISM(S): Mus musculus

PROVIDER: GSE55014 | GEO | 2014/03/21

SECONDARY ACCESSION(S): PRJNA238249

REPOSITORIES: GEO

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Identification of candidate genes regulated by E4bp4 in murine bone marrow

Project description:E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP Total RNA was extracted from linege-depleted bone marrow from six wild type and six E4bp4 knockout mice. Labelled cDNA was hybridised to a GeneChip Mouse Gene 1.0 ST Array. The data generated was imported into GeneSpring GXv11 (Agilent) and normalised using the Robust Multi-Array (RMA16) algorithm. Genes were filtered on expression value between 20th and 100th percentile to remove those with very low or no expression across all the samples. A moderated t-test was applied to the data and p values were adjusted for multiple testing using a Benjamini-Hochberg False Discovery Rate correction.

2014-03-21 | E-GEOD-55014 | biostudies-arrayexpress

ChIP-seq for E4BP4 in CD4+ T cell

Project description:Here, using ChIP-seq, we demonstrate that the transcriptional repressor Adenovirus E4 promoter-binding protein (E4BP4) binds directly to the Bcl6 promoter, which a key transcription factor controlling Tfh cell differentiation. By obtaining sequence from chromatin immunoprecipitated DNA of E4BP4 overexpressing CD4+T cells, we generated genome-wide binding gene spectrums of E4BP4. These results reveal that E4BP4 interacts with BCL6 and E4BP4 directly modulated the expression of Bcl6 to reveal the mechanism downstream of E4BP4 that regulates Tfh cell differentiation.

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Expression profiles of E4BP4 knockout RAW264.7 cells [RAW_KOvsWT_RNA-seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the gene expression of E4BP4 knockout (KO) RAW264.7 cells. Methods: We generated E4BP4-KO RAW264.7 Cell Line using CRISPR-CAS9 system. Control plasmid was encoding the Cas9 nuclease without gRNA sequence. Total RNA of E4BP4-KO and Control (CTRL) RAW264.7 cells was extracted. RAW264.7 cells RNA profiles were generated by deep sequencing for two groups (E4BP4-KO versus CTRL RAW264.7 cells) with three samples each. Results: There were significant differences between E4BP4-KO and CTRL RAW264.7 cells. Conclusions: Deletion of E4BP4 in RAW264.7 cells induced various changes at the transcription level.

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Differential requirement for Nfil3 during NK cell development

Project description:Natural killer (NK) cells can be grouped into distinct subsets that are localized to different organs and exhibit different capacity to secrete cytokines and mediate cytotoxicity. Despite these hallmarks that reflect tissue-specific specialization in NK cells, little is known about the factors that control the development of these distinct subsets. The basic leucine zipper transcription factor nuclear factor interleukin 3 (Nfil3; E4bp4) is essential for bone marrow-derived NK cell development but it is not clear whether Nfil3 is equally important for all NK cell subsets nor how it induces NK lineage commitment. Here we show that Nfil3 is required for the formation of Eomesodermin (Eomes)-expressing NK cells, including conventional medullary and thymic NK cells, whereas TRAIL+ Eomes- NK cells develop independent of Nfil3. Loss of Nfil3 during the development of bone marrow-derived NK cells resulted in reduced expression of Eomes and, conversely, restoration of Eomes expression in Nfil3-/- progenitors rescued NK cell development and maturation. Collectively, these findings demonstrate that Nfil3 drives the formation of mature NK cell by inducing Eomes expression and reveal the differential requirements of NK cell subsets for Nfil3. RNA-sequencing of natural killer (NK) cell subsets

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Hepatocyte E4BP4 promotes liver fibrosis via enhancing hepatic stellate cells activation

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ChIP-seq for E4BP4 in the liver from transgenic mouse with liver specific E4BP4 overexpression

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Project description:To identify hepatic genes specifically regulated by E4bp4. Lipid droplet binding genes are downregulated in the liver of E4bp4 liver specific knockout mice.

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Novel Roles for the Transcriptional Repressor E4BP4 in Both Cardiac Physiology and Pathophysiology

Project description:Circadian clocks temporally orchestrate biological processes critical for cellular/organ function. For example, the cardiomyocyte circadian clock modulates cardiac metabolism, signaling, and electrophysiology over the course of the day, such that, disruption of the clock leads to age-onset cardiomyopathy (through unknown mechanisms). Here, we report that genetic disruption of the cardiomyocyte clock results in chronic induction of the transcriptional repressor E4BP4. Importantly, E4BP4 deletion prevents age-onset cardiomyopathy following clock disruption. These studies also indicate that E4BP4 regulates both cardiac metabolism (eg, fatty acid oxidation) and electrophysiology (eg, QT interval). Collectively, these studies reveal that E4BP4 is a novel regulator of both cardiac physiology and pathophysiology.

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Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

Project description:ATACseq was performed by overexpressing E4BP4 in RAW264.7 cells using lentivirus.

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