Homo sapiens
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PROVIDER: PRJNA272552 | ENA |
REPOSITORIES: ENA
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Project description:Interplanetary human spaceflight represents a formidable medical challenge, but also provides a unique platform for investigating human adaptation to extreme environmental changes. Understanding the long-term effects of isolation has relevance in a range of scenarios and it is well recognized that a better understanding of the relationship between environmental exposure and the epigenome can lead to more effective preventive measures. Here we conduct a longitudinal epigenetic, mood state and biochemical profiling of 6 crew members in an experiment simulating a 520-day mission to Mars. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles. Firstly, we found that long-term isolation can induce global DNA methylation remodeling, and this change seems to be an active adaptation (rather than a random process or a by-product of the isolation). This study is the first to demonstrate the dynamic relationship between global epigenetic remodeling and isolation-induced mood state and biochemical changes. Secondly, by considering the location of methylation sites within the genome and using gene-pathway annotation, we were able to identify pathways that were significantly enriched in methylation events and consider their association with specific function and the timeline of the mission. Thirdly, via our definition of epi-entropy, a measure of entropy adapted to methylation events, we observed that the methylation remodeling produced a marked reduction in epi-entropy. Results suggest that DNA methylation change is an indicator of change rather than its by-product, i.e., there is a psychology-epigenome-metabolism model of long-term depression; DNA methylation programs the environment signal into the epigenome, which is subsequently transformed into the biochemical output and health outcome. Thus, longitudinal epigenetic profiling could code the effect of isolation and act as early indicators of latent health outcome. A longitudinal epigenetic, mood state and biochemical profiling of 6 crew members in an experiment simulating a 520-day mission to Mars. 36 samples of blood cell DNA methylation profiling were obtained by Illumina HumanMethylation450 BeadChip, across 6 sampling points during the 520 days mission for all of the 6 crew members.
2015-01-14 | E-GEOD-64950 | biostudies-arrayexpress
Project description:Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/ MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function. Contrast between DNA bound to nuclear scaffold/matrix and total genomic DNA in Arabidopsis Chr4 excluding the constitutive heterochromatin. Total of three biological replicates with two independent hybridizations on custom-designed NimbleGen high-density microarrays that include duplicate spots for each probe.
2014-02-03 | E-GEOD-45549 | biostudies-arrayexpress
Project description:In this study, we designed a space simulation study, named “4 Subjects 180-Day Controlled Ecological Life Support System (CELSS) Integration Experiment”, which took place in Shenzhen, China, from June to December 2016. In this experiment, four subjects (3 males and 1 female) lived for 180 days in an enclosed simulated cabin, and multiple-sampling-point DNA methylation data was collected to conduct the epigenic analysis. Peripheral whole blood cells were extracted from all 4 subjects on the 12 sampling points (Pre45, Pre15, R2, R30, R60, R75, R90, R105, R120, R150, R175 and Post30 mission day during the experiment).
2019-06-21 | GSE133118 | GEO
Project description:Abstract Background The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for one year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from Low Earth orbit, was performed. Methods We monitored Deinococcus radiodurans cells during early stage of recovery after Low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in Low Earth orbit. Results D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane associated vesicles was observed. On levels of proteins and transcripts, a multifaceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine which works as scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicate alternations in the energy status, which is needed to repair damaged molecules. Conclusion Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term Low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions.
2021-09-09 | PXD020047 | Pride
Project description:Eukaryotic genome is compartmentalized into structural and functional domains. One of the concepts of higher order organization of chromatin posits that the DNA is organized in constrained loops that behave as independent functional domains. A predominantly ribo-proteinaceous nucleoskeleton, termed as Nuclear Matrix (NuMat) is proposed to provide the structural platform for attachment of these loops. The DNA sequence located at the base of the loops are known as the Matrix Attachment Regions (MARs). NuMat relates to all nuclear processes and has been shown to be cell type specific in composition. It is a biochemically defined structure and several protocols have been used to isolate the NuMat where some of the steps have been critically evaluated. In the present study we have looked into the dynamics of MARs when the isolation process is varied and also during embryonic development of D. melanogaster. Our results show that a subset of MARs termed here as “Core-MARs” are fixed and unalterable anchor points in the Drosophila genome as they remain associated with NuMat at all developmental stages and do not depend on the isolation procedure used. Core-MARs are abundant in the pericentromeric heterochromatin. On the other hand, MARs in the euchromatin are dynamic and reflect the transcriptomic profile of the developmental stage of the host cell. New MARs are generated by nuclear stabilization (a critical step in the isolation procedure), and during development, mostly at the paused RNA polymerase II (Pol II) promoters. Paused Pol II MARs depend on RNA transcription for NuMat association. RNase A treatment leads to collapse of the NuMat and loss of paused Pol II promoter MARs. Our data reveals the role of MARs in functional compartmentalization of D. melanogaster genome and adds to the current understanding of nuclear architecture and 3D organization of a functionally dynamic nucleus.
2022-10-25 | PXD031279 | Pride
Project description:Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/ MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.
2014-02-03 | GSE45549 | GEO
Project description:Dynamic changes in tRNA modifications and abundance during T-cell activation [MARS-seq]
| PRJNA694917 | ENA
Project description:Clonal expansion and immunological memory are hallmark features of the mammalian adaptive immune response and essential for prolonged host control of pathogens. Recent work demonstrated that natural killer (NK) cells of the innate immune system also exhibit these adaptive traits during infection. Here we demonstrate that differentiating and ‘memory’ NK cells possess distinct chromatin accessibility states, and that their epigenetic profiles reveal a ‘poised’ regulatory program at the memory stage. Furthermore, we elucidate how individual STAT proteins differentially control epigenetic and transcriptional states early during infection. Finally, concurrent chromatin profiling of the canonical CD8+ T cell response against the same infection demonstrated parallel and distinct epigenetic signatures defining NK cells and CD8+ T cells. Overall, our study reveals the dynamic nature of epigenetic imprinting during the generation of innate and adaptive lymphocyte memory.
2018-05-29 | GSE108051 | GEO
Project description:In this report, we generated eight matched pairs of vemurafenib sensitive/resistant melanoma lines and subjected these to concurrent RNA-seq and H3K27Ac ChIP-seq analysis. Globally, we identified two classes of epigenetic profiles that correlate with resistance. Class 1 resistance involves fewer RNA expression alterations accompanied by fewer enhancer mark changes with H3K27Ac. Class 2 resistance shows widespread alterations in transcription and enhancer profiles, which converge on EMT and hypoxia-related pathways. We also observed significant and dynamic changes in super-enhancers that underpin these transcriptomic patterns. We subsequently verified the 2-class structure in pre-BRAFi and post-relapse human melanoma specimens. Our findings reveal a broad and underappreciated spectrum of epigenetic plasticity during acquired BRAFi resistance.
2022-05-25 | GSE203544 | GEO