Chromatin Immunoprecipitation Sequencing of histone modifications (H3K4me3 and H3K27ac) in mouse macrophages (RAW264.7) infected with Mycobacterium tuberculosis
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE290166 | GEO | 2025/09/01
REPOSITORIES: GEO
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Project description:Transcriptional profiling of RAW264.7 cells infected with M. tuberculosis H37Rv at an MOI of 10 performed 4 and 24 hours post-infection.
2014-12-23 | GSE64427 | GEO
Project description:Transcriptional profiling of RAW264.7 cells infected with M. tuberculosis H37Rv at an MOI of 10 performed 4 and 24 hours post-infection. RAW264.7 cells were infected with Mtb for 4 hours at an MOI of 10. Cells were washed and treated with gentamycin for 2 hours in order to remove adhered bacteria. Incubation was continued further for 4 and 24 hours followed by total RNA isolation. Total RNA was labelled with Agilent’s quick-Amp labelling kit (p/n: 5190-0444) to generate fluorescent complementary RNA by using T7 promoter based linear amplification. The control sample was labelled with Cy3 while the infected samples were labelled with Cy5 and hybridized to an Agilent oligo microarray kit.
2014-12-23 | E-GEOD-64427 | biostudies-arrayexpress
Project description:BACKGROUND: Histone modification is an epigenetic mechanism that influences gene regulation in eukaryotes. In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. Changes in gene expression play a crucial role in adaptation and evolution. RESULTS: In this paper, we have studied, using a computational biology approach, the relationship between histone modifications in CGIs and selective pressure in Homo sapiens. We considered three histone modifications: histone H3 lysine 4 trimethylation (H3K4me3), histone H3 lysine 27 acetylation (H3K27ac) and histone H3 lysine 36 trimethylation (H3K36me3), and we used the publicly available genomic-scale histone modification data of thirteen human cell lines. To define regions under selective pressure, we used three distinct signatures that mark selective events from different evolutionary periods. We found that CGIs under selective pressure showed significant enrichments for histone modifications. CONCLUSION: Our result suggests that, CGIs that have undergone selective events are characterized by epigenetic signatures, in particular, histone modifications that are distinct from CGIs with no evidence of selection.
| S-EPMC3711888 | biostudies-other
Project description:Perturbation of host physiology by intracellular Mycobacterium tuberculosis (H37Rv) can be reflected by changes in gene expression pattern of host genes. Total RNA was isolated from PMA differentiated uninfected cells or cells infected with H37Rv for 16, 48 or 90 hours and gene expression profile was obtained.
2010-05-01 | GSE19052 | GEO
Project description:Wild house mice form social hierarchies with aggressive males defending territories, in which females, young mice and submissive adult males share nests. In contrast, socially excluded males are barred from breeding groups, have numerous bite wounds and patches of thinning fur. Since their feeding times are often disrupted, we investigated whether social exclusion leads to changes in epigenetic marks of metabolic genes in liver tissue. We used chromatin immunoprecipitation and quantitative PCR to measure enrichment of two activating histone marks at 15 candidate loci. The epigenetic profiles of healthy males sampled from nest boxes differed significantly from the profiles of ostracized males caught outside of nests and showing bite wounds indicative of social exclusion. Enrichment of histone-3 lysine-4 trimethylation (H3K4me3) changed significantly at genes Cyp4a14, Gapdh, Nr3c1, Pck1, Ppara, and Sqle. Changes at histone-3 lysine-27 acetylation (H3K27ac) marks were detected at genes Fasn, Nr3c1, and Plin5. A principal components analysis separated the socialized from the ostracized mice. This was independent of body weight for the H3K4me3 mark, and partially dependent for H3K27ac. There was no separation, however, between healthy males that had been sampled from two different nests. A hierarchical cluster analysis also separated the two phenotypes, which was independent of body weight for both markers. Our study shows that a period of social exclusion during adult life leads to quantitative changes in histone modification patterns in mouse liver tissue. Similar epigenetic changes might occur during the development of stress-induced metabolic disorders in humans.
| S-EPMC4534140 | biostudies-literature
Project description:The outcome of many infections depends on the initial interactions between agent and host. Aiming at elucidating the effect of the M. tuberculosis Mce1 protein complex on host transcriptional and immunological responses to infection with M. tuberculosis, RNA from murine macrophages at 15, 30, 60 min, 4 and 10 hrs post-infection with M. tuberculosis H37Rv or mce1 H37Rv was analyzed by whole-genome microarrays and RT-QPCR. Immunological responses were measured using a 23-plex cytokine assay. Compared to uninfected controls, 524 versus 64 genes were up-regulated by 15min post H37Rv- and mce1 H37Rv-infection, respectively. By 15min post-H37Rv infection, a decline of 17 cytokines combined with up-regulation of Ccl24 (26.5-fold), Clec4a2 (23.2-fold) and Ppar (10.5-fold) indicated an anti-inflammatory response initiated by IL-13. Down-regulation of Il13ra1 combined with up-regulation of Il12b (30.2-fold), suggested switch to a pro-inflammatory response by 4hrs post H37Rv-infection. Whereas no significant change in cytokine concentration or transcription was observed during the first hour post mce1 H37Rv-infection, a significant decline of IL-1b, IL-9, IL-13, Eotaxin and GM-CSF combined with increased transcription of Il12b (25.1-fold) and Inb1 (17.9-fold) by 4hrs, indicated a pro-inflammatory response. The balance between pro-and anti-inflammatory responses during the early stages of infection may have significant bearing on outcome.
2011-10-05 | E-TABM-1170 | biostudies-arrayexpress
Project description:While previous studies have shown that histone modifications could influence plant growth and development by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), to investigate the genome-wide distribution of four histone modifications: di and trimethylation of H3K4 (H3K4me2 and H3K4me3) and acylation of H3K9 and H3K27 (H3K9ac and H3K27ac) in Oryza sativa L. japonica. By analyzing published DNase-Seq data, this study explored DNase-Hypersensitive (DH) sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites (TSSs) of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.
| S-EPMC3842134 | biostudies-literature
Project description:Macrophage balance is important in several diseases. Raw 264.7 is a macrophage cell line. We previous detected that sialin (encoded by Slc17a5) play a key role in modulation of Raw264.7 which induced by LPS&IFNγ(M1 cells, proinflammatory cells) or IL4(M2 cells,anti-proinflammatory cells). Results showed nitrate could decrease the pro-inflammatory Raw264.7 cells while increase anti-inflammatory Raw26.7 cells. We transfected sialin overexpression plasmid to Raw264.7 and found that sialin could directly modulates Raw264.7 without nitrate. In this study, we want to figure out which genes could be the key factor modulated by sialin.
2025-08-05 | GSE248235 | GEO
Project description:We report the application of RNA-seq technology for high-throughput profiling of gene transcription in RAW264.7 infected with Mycobacterium tuberculosis H37Ra. By obtaining over six billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra. We find that numerous genes involved in ER stress are significantly affected by CdhM. This finding indicates that CdhM may induce ER stress during Mtb infection of host cells.
2022-02-24 | GSE196961 | GEO
Project description:Background. Recent epigenomic studies have shown that the length of a DNA region covered by an epigenetic mark is not just a byproduct of the assaying technologies and has functional implications for that locus. For example, expanded regions of DNA sequences that are marked by enhancer-specific histone modifications, such as acetylation of histone H3 lysine 27 (H3K27ac) domains coincide with cell-specific enhancers, known as super or stretch enhancers. Similarly, promoters of genes critical for cell-specific functions are marked by expanded H3K4me3 domains in the cognate cell type, and these can span DNA regions from 4-5kb up to 40-50kb in length. These expanded H3K4me3 domains are known as buffer domains or super promoters. Methods. To ask what correlates with-and potentially regulates-the length of loci marked with these two important histone marks, H3K4me3 and H3K27ac, we built Random Forest regression models. With these models, we computationally identified genomic and epigenomic patterns that are predictive for the length of these marks in seven ENCODE cell lines. Results. We found that certain epigenetic marks and transcription factors explain the variability of the length of H3K4me3 and H3K27ac marks across different cell types, which implies that the lengths of these two epigenetic marks are tightly regulated in a given cell type. Our source code for the regression models and data can be found at our GitHub page: https://github.com/zubekj/broad_peaks. Discussion. Our Random Forest based regression models enabled us to estimate the individual contribution of different epigenetic marks and protein binding patterns to the length of H3K4me3 and H3K27ac deposition patterns, therefore potentially revealing genomic signatures at cell specific regulatory elements.
| S-EPMC4793332 | biostudies-literature