Gallus gallus
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ABSTRACT:
PROVIDER: PRJNA101571 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression in Histone H1 variant deletion chicken DT40 mutant cell
| PRJNA96605 | ENA
Project description:In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804]) but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities (Hashimoto et al., DNA repair (2007) [17613284]), so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Next we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analysis those gene expression pattern in wild-type, K11, and K11-5 cells (Hashimoto et al., NAR (2010), PMID:20156997) Keywords: gene expression array-based, count
2008-05-01 | GSE8483 | GEO
Project description:In chicken DT40 cells, there are six linker histone H1 variants and 12 of coding genes. We have previously reported of 11 out of 12 H1 knock out DT40 cells (Takami et al., Genes to Cell 1997 [PMID:9491804]) but complete H1 null DT40 cells could not established, so far. We identified one of the H1 variant, H1R was involved in genomic instabilities (Hashimoto et al., DNA repair (2007) [17613284]), so we re-introduced floxed H1R-eGFP and mer-cre-mer into 11 out of 12 H1 knock out DT40 cells. Then we targeted last enedogenous H1, we successfully established conditional H1 KO cells (K11). Next we treated with tamoxifen to loop out floxed H1R-eGFP, and cloning H1 completely null cells (K11-5, and K11-7). We analysis those gene expression pattern in wild-type, K11, and K11-5 cells Experiment Overall Design: Apoptosis is induced in H1 null cells, so we inhibit apoptosis with pan-caspase inhibitor, Z-VAD-FMK and extract RNAs.
2008-11-04 | E-GEOD-8483 | biostudies-arrayexpress
Project description:There are six histone H1 variant in chicken. 01H1/02H1/03H1/.10H1/H1L and H1R. In those variant we forcused on H1L and H1R those molecule were most similar H1 among six H1 variants. we established linker histone H1L and H1R deleted mutant in chicken B-cell derived DT40 cell and assay gene expression in normal condition in those mutant cells. The detail charactalization of those mutant cell was published in Takami et al., BBRC 268, 501-508 (2000) and Hashimoto et al., DNA repair (2007) Keywords: gene expression array-based, count
2007-03-21 | GSE5114 | GEO
Project description:There are six histone H1 variant in chicken. 01H1/02H1/03H1/.10H1/H1L and H1R. In those variant we forcused on H1L and H1R those molecule were most similar H1 among six H1 variants. we established linker histone H1L and H1R deleted mutant in chicken B-cell derived DT40 cell and assay gene expression in normal condition in those mutant cells. The detail charactalization of those mutant cell was published in Takami et al., BBRC 268, 501-508 (2000) and Hashimoto et al., DNA repair (in press) Experiment Overall Design: There are six linker histone H1 variant in chicken. Linker histone was thought to be general gene supplesser. We established linker histone H1 variant mutant in chicken B-cell derived DT40 cell, and analyze total protein by 2D-PAGE to find up- or down- regulatd protein. In these mutant, there are some up regulated protein expression and down regulated protein expression (Takami et al., BBRC 268, 501-508 (2000), PubMedID 10679234). Experiment Overall Design: These 2D-PAGE experiment were limited at low density protein region, we use Affymetrix array to search the gene that were regulated specific linker histone H1 variant mutant. Experiment Overall Design: We assayed total gene expression profile in H1L and H1R deleted mutant cells. Experiment Overall Design: all mutant cells were cultured in normal culture condition in RPMI 1640 medium supplemented with 10 µM 2-mercaptoethanol, 10% FCS (Biowest) and 1% chicken serum (Gibco) at 39.5ËC. Total RNA were isolated from exponently growing DT40 cells.
2008-11-08 | E-GEOD-5114 | biostudies-arrayexpress
Project description:In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create an h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.
2021-03-26 | GSE146948 | GEO
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (sh120) or multiple H1 variants (sh225), or overexpressing WT or K26A mutant HA-tagged H1.4.
2014-05-16 | GSE55786 | GEO
Project description:Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1, in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. However, the ratio of HMGD1 to H1 is better correlated with chromatin accessibility, gene expression and nucleosome spacing variation than either protein alone suggesting a competitive mechanism between these proteins. Indeed, we show that HMGD1 and H1 compensate each other’s absence by binding reciprocally to chromatin resulting in changes to nucleosome repeat length and distinct gene expression patterns. Collectively our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study thus provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation. ChIP-seq of HMGD1 and Histone H1 bound nucleosomes as well as MNase-seq of total nucleosome in Drosophila S2 cells
2013-12-01 | E-GEOD-49526 | biostudies-arrayexpress
Project description:MNase analysis of linker histone H1 mutant
| PRJNA451507 | ENA
Project description:Transcriptiomic analysis of linker histone H1 mutant
| PRJNA451508 | ENA