Conservation of global DNA methylation patterns due to cell culture establishment from human melanoma tissue
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE159741 | GEO | 2020/10/22
REPOSITORIES: GEO
Similar Datasets
Project description:Conservation of global DNA methylation patterns due to cell culture establishment from human melanoma tissue
| PRJNA670372 | ENA
Project description:Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.
2021-08-26 | GSE182772 | GEO
Project description:The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions. A total of 88 samples (16 normal colon tissues taken from adjacent tumor tissue, 70 colorectal tumor tissues and 2 cell lines) was analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features and copy number.
2012-08-31 | E-GEOD-35508 | biostudies-arrayexpress
Project description:<p>Aberrant DNA methylation changes are known to occur during prostate cancer progression beginning with precursor lesions. Utilizing fifty nanograms of genomic DNA in Methylplex-Next Generation Sequencing (M-NGS) we mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2). Peaks were located from mapped reads obtained in each sequencing run using a Hidden Markov Model (HMM)-based algorithm previously used for Chip-Seq data analysis(<a href="http://www.sph.umich.edu/csg/qin/HPeak">http://www.sph.umich.edu/csg/qin/HPeak</a>). The total methylation events in intergenic/intronic regions between benign adjacent and cancer tissues were comparable. Promoter CGI methylation gradually increased from -12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues and approximately 20% of all CpG islands (CGIs) (68,508) were methylated in tissues. We observed distinct patterns in promoter methylation around transcription start sites, where methylation occurred directly on the CGIs, flanking regions and on CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific and several previously studied targets were among them. A novel cancer specific DMR in WFDC2 promoter showed 77% methylation in cancer (17/22), 100% methylation in transformed prostate cell lines (6/6), none in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested a role for DNA methylation in alternate transcription start site utilization. While methylated promoters containing CGIs had mutually exclusive H3K4me3 modification, the histone mark was absent in CGI sparse promoters. Finally, we observed difference in methylation of LINE-1 elements between transcription factor ERG positive and negative cancers. The comprehensive methylome map presented here will further our understanding of epigenetic regulation of the prostate cancer genome. Overall Design: We mapped the global DNA methylation patterns in prostate tissues (n=17) and cells (n=2) from fifty nanograms of genomic DNA using Methylplex-Next Generation Sequencing (M-NGS). For replicate analysis in cell lines, a total of 4 runs were completed for PrEC prostate normal cell line, and 5 runs were completed for LNCaP prostate cancer cell line. For tissue samples, 2 benign prostate samples were sequenced twice on Illumina next generation sequencing platform to access overall repeatability of M-NGS.</p>
| phs000597 | dbGaP
Project description:The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. We observed that whereas histone modifications vary both between tissues and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between tissues. Histone modifications were associated with transcriptomic divergence between tissues and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements (TEs), and for different TEs in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species. Together, our results suggest that despite of the variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different tissues of maize hybrids. Genome-wide integrated maps of mRNA and small RNA (sRNA) transcriptomes, DNA methylomes and genome-wide distribution of three representative histone modifications (H3K4me3, H3K9ac and H3K36me3) in the shoots and roots of 14 day old seedlings of two maize inbred lines (B73 and Mo17) and their reciprocal hybrids (B73 x Mo17 and Mo17 x B73).
2013-03-19 | E-GEOD-43142 | biostudies-arrayexpress
Project description:DNA methylation patterns are set up in a relatively fixed programmed manner during normal embryonic development and are then stably maintained. Using genome-wide analysis, we have discovered a postnatal pathway involving gender-specific demethylation that occurs exclusively in the male liver. This demodification is programmed to take place at tissue-specific enhancer sequences, and our data show that the methylation state at these loci is associated with and appears to play a role in the transcriptional regulation of nearby genes. This process is mediated by the secretion of testosterone at the time of sexual maturity, but the resulting methylation profile is stable and therefore can serve as an epigenetic memory even in the absence of this inducer. These findings add a new dimension to our understanding of the role of DNA methylation in vivo and provide the foundations for deciphering how environment can impact on the epigenetic regulation of genes, in general. DNA methylation profile of male and female mouse and Human tissues was generated using the RRBS protocol followed by deep sequncing. Whole genome DNA methylation profile using deep sequencing was genereted for male and female mouse tissues. RNAseq was performed on male and female mouse tissues.
2015-05-03 | E-GEOD-60012 | biostudies-arrayexpress
Project description:The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. We observed that whereas histone modifications vary both between tissues and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between tissues. Histone modifications were associated with transcriptomic divergence between tissues and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements (TEs), and for different TEs in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species. Together, our results suggest that despite of the variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different tissues of maize hybrids.
2013-03-19 | GSE43142 | GEO
Project description:Genome-wide DNA methylation profiles were determined on a set of fresh 44 bladder cancer tissues using normal blood as control. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Agilent Human CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of bladder cancer along with finding markers for progresssion and early diagnosis. 44 bladder cancer tissues were profiled against commercially available normal human genomic blood DNA (Promega, Madison, WI, USA) as a reference
2012-02-16 | E-GEOD-35824 | biostudies-arrayexpress
Project description:The mammalian blastocyst consists of three distinct cell types: epiblast, trophoblast, and primitive endoderm (PrE). Although stem cell lines that retain functional properties of epiblasts or trophoblasts have been established, establishment of stem cell lines that fully retain developmental potential of PrE has long been awaited. Here we report derivation of primitive endoderm stem (PrES) cells, which are capable to give rise functional PrE derived tissues and support fetal development of PrE-depleted blastocysts in chimeras, in mice.
2021-12-31 | GSE159183 | GEO