Unknown,Transcriptomics,Genomics,Proteomics

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Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

ABSTRACT: Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed amplification of targeted sequences from sub-microgram input quantities of genomic DNA followed by next generation bisulfite sequencing. This provides highly scalable and simultaneous mapping of chromatin accessibility and DNA methylation on single molecules at high resolution. Long sequencing reads from targeted regions maintains the structural integrity of epigenetic information and provides substantial depth of coverage, detecting for the first time minority subpopulations of epigenetic configurations formerly obscured by existing genome-wide and population-ensemble methodologies. Analyzing a cohort of 71 promoters of genes with exons commonly mutated in cancer, MAPit-patch uncovered several differentially accessible and methylated promoters that are associated with altered gene expression between neural stem cell (NSC) and glioblastoma (GBM) cell populations. Additionally, substantial epigenetic heterogeneity was observed across the sequenced molecules at individual promoters, indicating the presence of epigenetically distinct cellular subpopulations. This study includes 4 samples, NSC probed with 100U M.CviPI and 0U control; GBM probed with 100U M.CviPI and 0U control.

ORGANISM(S): Homo sapiens

SUBMITTER: Nancy Nabilsi

PROVIDER: E-GEOD-50047 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer inputs such as organic agriculture and natural ecosystems by extending the effective size of the rhizosphere and delivering mineral. Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic. This study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N). A wild-type mycorrhizal tomato and a closely-related nonmycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community. The majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and nonmycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes. However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root supplied N. Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions. A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters. These results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture. 30 samples were analyzed. There were 2 genotypes (wildtype and mutant) and 3 treatments (two N treatments and a water control) for a total of 6 groups. Each group had 5 biological replicates.

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Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

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