The bovine alveolar macrophage (bAM) DNA methylome is resilient to infection with Mycobacterium bovis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA433673 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6704030_1.fastq.gz | Fastqsanger.gz | |||
| SRR6704030_2.fastq.gz | Fastqsanger.gz | |||
| SRR6704040_1.fastq.gz | Fastqsanger.gz | |||
| SRR6704040_2.fastq.gz | Fastqsanger.gz | |||
| SRR6704050_1.fastq.gz | Fastqsanger.gz |
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Project description:Whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome (5-methylcytosine). The methylomes of bAM infected with M. bovis (n = 8) were compared to those of non-infected control bAM (n = 8) at 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed between control and infected bAM. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation = 33–66%). Gene ontology (GO) analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of two non-imprinted genes in the IM category, C1QB and IL2RA, confirmed the WGBS observation. This study is the first in cattle to examine genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model and provides evidence for intermediate promoter methylation in bAM.
2019-02-13 | GSE110412 | GEO
Project description:Bovine tuberculosis, caused by Mycobacterium bovis, is a disease of considerable economic importance yet comparatively little is known about the bovine immune response to the disease. Alveolar macrophages are one of the first cells to encounter mycobacteria following infection. In this experiment we investigated the early transcriptional response of bovine alveolar macrophages following infection with M. bovis. The transcriptional response to heat-killed M. bovis was also investigated to look for genes that are only differentially transcribed in response to the live organism. Five-condition experiment, uninfected, live and heat-killed M. bovis-infected bovine alveolar macrophages from five cattle infected for two and four hours. Comparisons were within animal. Dye swaps were incorporated into the design.
2010-01-30 | E-GEOD-19237 | biostudies-arrayexpress
Project description:DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33-66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
| S-EPMC6365515 | biostudies-literature
Project description:Bovine tuberculosis, caused by Mycobacterium bovis, is a disease of considerable economic importance yet comparatively little is known about the bovine immune response to the disease. Alveolar macrophages are one of the first cells to encounter mycobacteria following infection. In this experiment we investigated the early transcriptional response of bovine alveolar macrophages following infection with M. bovis. The transcriptional response to heat-killed M. bovis was also investigated to look for genes that are only differentially transcribed in response to the live organism.
2010-01-31 | GSE19237 | GEO
Project description:Here we present HDX-MS data to study the conformational dynamics of BAM, BAM(T434A) and BAM(LVPR).
2025-10-13 | PXD057055 | Pride
Project description:Abstract: During Drosophila oogenesis, germline stem cell (GSC) identity is maintained largely by preventing the expression of factors that promote differentiation. This is accomplished via the activity of several genes acting either in the GSC or its niche. The translational repressors, Nanos and Pumilio, act in GSCs to prevent differentiation, likely by inhibiting translation of early differentiation factors, while niche signals prevent differentiation by silencing transcription of the differentiation factor Bam. We have found that the DNA-associated protein Stonewall (Stwl) is also required for GSC maintenance. stwl is required cell-autonomously; clones of stwl- germ cells were lost by differentiation, and ectopic Stwl caused an expansion of GSCs. stwl mutants acted as Suppressors of Variegation, indicating stwl normally acts in chromatin-dependent gene repression. In contrast to several previously described GSC maintenance factors, Stwl likely functions epigenetically to prevent GSC differentiation. Stwl-dependent transcriptional repression does not target bam, but rather Stwl represses the expression of many genes, including those that may be targeted by Nanos/Pumilio translational inhibition. Experiment Overall Design: Genetic variation comparison between germ cells of Drosophila ovaries from bam mutant and stwl bam double mutant females. Six total samples were analyzed, with each genotype performed in triplicates.
2008-03-13 | E-GEOD-6928 | biostudies-arrayexpress
Project description:Purpose: The goal of this RNA-seq study was to profile changes in miRNA expression in bovine alveolar macrophages isolated from Holstein-Friesian and challenged with M. bovis over a 48 hour time course. Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major infectious disease problem for global agriculture, resulting in losses of billions of Euros annually. The bacterium spreads via an airborne route and is taken up by alveolar macrophages in the lung. MicroRNAs (miRNAs) — short non-coding RNAs that post-transcriptionally regulate gene expression — are increasingly being recognised as key regulators of the immune system. There is mounting evidence for the role of miRNAs in regulating the early innate immune response to mycobacterial infections; however, the underlying processes are not fully understood yet. Results: In total, 2.5 billion raw sequencing reads were generated. 93% of post-filtered reads aligned to known miRNAs. The expression of miRNAs varied over a wide range: miR-21 was expressed at approximately 430,000 reads per million (RPM), but the majority were more lowly expressed (1000-10,000 RPM). One, six, and 40 miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection (hpi), respectively (FDR < 0.05); the differential expression at 48 hpi of three (out of four) of these miRNAs was confirmed by RT-qPCR. No miRNAs were detected to be differentially expressed 6 hpi. Many of the differentially expressed miRNAs have been shown to have a role in the host response to mycobacterial pathogens and other infections in other species. MicroRNA-155, for example, which we observed to be upregulated in response to M. bovis has recently been shown to control autophagy in murine macrophages infected with the human pathogen Mycobacterium tuberculosis. Pathway analysis suggests that upregulated miRNAs target endocytosis and lysosome trafficking, thus potentially enhancing bacterial survival. An independent gene silencing experiment with a bovine macrophage cell line (Bomac) has confirmed downregulation of IRAK1 by miR-146a and miR-146b. Moreover, downregulation of another predicted target, TGFRB2, by miR-146a was also confirmed. These findings support the target prediction and pathway analysis results. Our results suggest that several miRNAs have an important role in the alveolar macrophage response to pathogenic mycobacteria.
2014-11-13 | GSE58883 | GEO
Project description:Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms.
2015-10-10 | GSE62506 | GEO