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DNA methylation signatures reveal the diversity of processes remodeling liver cancer methylomes

ABSTRACT: DNA methylation signatures reveal the diversity of processes remodeling liver cancer methylomes

PROVIDER: PRJNA661028 | ENA |

REPOSITORIES: ENA

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DNA methylation signatures reveal the diversity of processes remodeling liver cancer methylomes

Project description:Genome-scale DNA methylation was analyzed in a cohort of 239 hepatocellular adenomas and 35 normal liver tissues.

2020-09-03 | GSE157341 | GEO

Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

Project description:Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

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Tissue-specific methylomes reveal epigenetic memory in adult mouse tissue

Project description:Cytosine methylation of DNA is an evolutionarily conserved mechanism from plants to animals with crucial roles in gene regulation. However, the variation between methylomes of normal tissues is largely unexplored. To better understand the epigenetic variation of a normal individual, we profiled DNA methylation using whole genome bisulfite sequencing in 17 tissues isolated from an individual mouse. We observed a unique distribution of CpG methylation for each tissue, which cluster based on cell lineage. Global analysis identified only one-eighth of the genome as tissue-specifically methylated. Remarkably, the vast majority of these regions exhibit hallmarks of cis-regulatory activity. Our results also reveal a novel class of dormant enhancers in adult tissues which retain an epigenetic memory of regulatory elements active during development. Together, these results expand the repertoire of regulatory information encoded within the methylome, and suggest mapping it as an alternative method to identify cell-type specific regulatory elements. whole genome bisulfite sequencing of mouse adult tissue

2013-09-01 | E-GEOD-42836 | biostudies-arrayexpress

Diet-induced circadian enhancer remodeling synchronizes opposing hepatic lipid metabolic processes

Project description:Diet-induced circadian enhancer remodeling synchronizes opposing hepatic lipid metabolic processes

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Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation.

Project description:X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is an iconic example of epigenetic regulation. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here, we examine genome-wide signatures of DNA methylation across fives tissues from a male and female koala (Phascolarctos cinereus), and present the first whole-genome, multi-tissue marsupial 'methylome atlas'. Using these novel data, we elucidate divergent versus common features of representative marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in koalas primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx, the primary lncRNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-specific (and presumably inactive X chromosome-specific) expression. Finally, we use the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5%) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily divergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.

| S-EPMC7934952 | biostudies-literature

Tissue-specific methylomes reveal epigenetic memory in adult mouse tissue

2013-09-01 | GSE42836 | GEO

Transcriptomic insight into molecular processes of dorsal muscle remodeling during Microhyla fissipes metamorphosis

Project description:Transcriptomic insight into molecular processes of dorsal muscle remodeling during Microhyla fissipes metamorphosis

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Divergences of sperm DNA methylomes between monozygotic twin seed bulls reveal fertility-related genes

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The DNA methylomes of serous borderline tumours reveal subgroups with malignant-like or benign-like profiles

Project description:Serous borderline tumours (SBOT) are a challenging group of ovarian tumours positioned between benign and malignant disease. We have profiled the DNA methylomes of 12 low grade serous carcinoma (LGSC), 19 SBOT and 16 benign serous tumours (BST) across 27,578 CpG sites to further characterise the epigenomic relationship between these subtypes of ovarian tumours. Unsupervised hierarchical clustering of DNA methylation levels showed that LGSC differ distinctly from BST, however, not from SBOT. Gene ontology analysis of genes showing differential methylation at linked CpG sites between LGSC and BST revealed significant enrichment of gene groups associated with cell adhesion, cell-cell signalling and the extracellular region consistent with a more invasive phenotype of LGSC as compared to BST. Consensus clustering highlighted differences between SBOT methylomes and returned subgroups with malignant-like or benign-like methylation profiles. Furthermore, a two loci DNA methylation signature can distinguish between these SBOT subgroups with benign-like and malignant-like methylation characteristics. Our findings indicate striking similarities between SBOT and LGSC methylomes which supports a common origin and the view that LGSC may arise from SBOT. A subgroup of SBOT can be classified into tumours with a benign-like or a malignant-like methylation profile which may help in identifying tumours more likely to progress into LGSC. Array-based methylation profiling was performed using the Infinium HumanMethylation27 BeadChip in 12 low grade serous carcinoma, 19 serous borderline tumours and 16 benign serous tumours. The reproducibility of the Infinium HumanMethylation27 BeadChips was evaluated using four biological replicates of the high grade serous ovarian cancer cell line PEO1. Differential methylation cutoff was estimated from four biological replicates by bootstrap resampling and set at Δβ ≥ 0.25 corresponding to a FDR ≤ 0.09.

2012-12-31 | E-GEOD-40105 | biostudies-arrayexpress

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