Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in chronic lymphocytic leukemia

ABSTRACT: Cancer evolution is fueled by genetic and epigenetic diversity, and intra-tumoral heterogeneity in DNA methylation has been shown to co-operate with genetic heterogeneity to empower evolutionary capacity of cancers such as chronic lymphocytic leukemia. Here, we show that epigenetic diversification leads to decreased coordination across layers of epigenetic information, likely reflecting an admixture of cells with diverging epigenetic identities. This manifests in incomplete gene silencing by the Polycomb complex, unexpected co-occurrence of typically mutually exclusive activating and repressing histone modifications, and greater cell-to-cell transcriptional heterogeneity.

ORGANISM(S): Homo sapiens

PROVIDER: GSE119103 | GEO | 2019/05/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in chronic lymphocytic leukemia

Project description:Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in chronic lymphocytic leukemia

| PRJNA488107 | ENA

Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders

Project description:Comparison of conserved TAD boundaries reveals that diverging CTCF sites is an evolutionary conserved signature associated with TAD borders 4C-seq samples for six gene family promoters in different samples: E9.5 and E14.5 mouse embryos ; 24hpf, 48hpf, 80%epiboly and Dome zebrafish embryos ; 48hpf S.purpuratus embryos

2015-05-18 | E-GEOD-66900 | biostudies-arrayexpress

Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders

Project description:Comparison of conserved TAD boundaries reveals that diverging CTCF sites is an evolutionary conserved signature associated with TAD borders

2015-05-18 | GSE66900 | GEO

Earliest Diverging Fungi and Rotosphaerida in Beijing

Project description:Earliest Diverging Fungi and Rotosphaerida in China Raw sequence reads

| PRJNA848264 | ENA

Pachytene piRNA Genes Are Rapidly Diverging Among Modern Humans

Project description:In the fetal mouse testis, PIWI Interacting RNAs (piRNAs) guide PIWI proteins to silence transposons, but after birth, most post-pubertal pachytene piRNAs map to genome uniquely and are thought to regulate genes required for male fertility. In human males, the developmental classes, precise genomic origins, and transcriptional regulation of post-natal piRNAs remain undefined. Here, we demarcate the genes and transcripts that produce post-natal piRNAs in human juvenile and adult testes. As in mouse, A‑MYB in humans drives transcription of both pachytene piRNA precursor transcripts and the mRNAs encoding piRNA biogenesis factors. Although human piRNA genes are syntenic to those in other placental mammals, their sequences are poorly conserved. In fact, pachytene piRNA loci are rapidly diverging even among modern humans. Our findings suggest that during mammalian evolution, pachytene piRNA genes are under fewer selective constraints. We speculate that pachytene piRNA diversity may provide a hitherto unrecognized driver of reproductive isolation.

2019-12-23 | GSE135791 | GEO

Diverging principles of selective sex chromosome regulation during evolution of Drosophila

Project description:Diverging principles of selective sex chromosome regulation during evolution of Drosophila

| PRJNA698339 | ENA

ProteoMixture: A Cell Deconvolution Tool for Bulk Tissue Proteomics Data

Project description:Numerous multi-omic investigations of cancer tissue have documented varying and poor pairwise transcript:protein quantitative correlations and most deconvolution tools aiming to predict cell type proportions (cell admixture) have been developed and credentialed using transcript-level data alone. To estimate cell admixture using protein abundance data, we analyzed proteome (and transcriptome data) generated from contrived admixtures of tumor, stroma, and immune cell models or those selectively harvested from the tissue microenvironment by laser microdissection from high grade serous ovarian cancer (HGSOC) tumors. Co-quantified transcripts and proteins performed similarly to estimate stroma and immune cell admixture in two commonly used deconvolution algorithms ESTIMATE and ConsensusTME (r ≥ 0.63). Here we have developed and optimized protein-based signatures to estimate cell admixture proportions and benchmarked these using bulk tumor proteomics data from over 150 HGSOC patients. The optimized protein signatures supporting cell type proportion estimates from bulk tissue proteomic data are available at https://lmdomics.org/ProteoMixture/.

2024-01-12 | PXD044157 | Pride

Prediction of outcomes and response to treatments with an ultrasensitive method for assessing intratumor epigenetic heterogeneity in colorectal cancer

Project description:Primary outcome(s): The detection rates of epigenetic heterogeneity in primary tumor and plasma from colorectal cancer patients with Methylation-sensitive high resolution melt(MS-HRM).

| 2636460 | ecrin-mdr-crc

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ChIP-Seq]

Project description:Despite deep evolutionary conservation, recombination varies greatly across the genome, among individuals, sexes and populations and can be a major evolutionary force in the wild. Yet this variation in recombination and its impact on adaptively diverging populations is not well understood. To elucidate the nature and potential consequences of recombination rate variation, we characterized fine-scale recombination landscapes by combining pedigrees, functional genomics and field fitness measurements in an adaptively divergent pair of marine and freshwater threespine stickleback populations from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic location of almost 50,000 crossovers and built recombination maps for 36 marine, freshwater, and hybrid individuals at 3.8 kilobase resolution. Using these maps, we quantified the factors driving variation in recombination rate: we find strong heterochiasmy between sexes (68% of the variation) but also differences among ecotypes (21.8%). Hybrids show evidence of significant recombination suppression, both in overall map length and in individual loci. We further tested and found reduced recombination rates both within single marine–freshwater adaptive loci and between loci on the same chromosome, suggestive of selection on linked ‘cassettes’. We tested theory supporting the evolution of linked selection using temporal sampling along a natural hybrid zone, and found that recombinants with shuffled alleles across loci show traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers whose mechanisms are disrupted in hybrids, may have an important role to play in the maintenance of differences among adaptively diverging populations.

2024-05-24 | GSE254557 | GEO

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ATAC-Seq]

2024-08-01 | GSE254559 | GEO