Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA hypomethylation comprising transposable elements defines human regulatory T cells in cutaneous tissue and identifies their blood recirculating counterpart

ABSTRACT: DNA hypomethylation comprising transposable elements defines human regulatory T cells in cutaneous tissue and identifies their blood recirculating counterpart

PROVIDER: PRJNA1210589 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

DNA hypomethylation comprising transposable elements defines human regulatory T cells in cutaneous tissue and identifies their blood recirculating counterpart

Project description:Regulatory T cells (Treg cells) in tissues play crucial immunoregulatory and tissue-regenerative roles. Despite their significance, the epigenetic basis of human tissue-Treg cells, their differentiation as well as a migratory subset of tissue-Treg cells are incompletely understood. Here, we performed genome-wide DNA methylation analysis of human Treg cells from skin and blood and integrated these data into a multi-omic framework including chromatin accessibility and gene expression. This analysis revealed novel programs governing human skin Treg cell differentiation and delineated the presence of these programs across molecular levels. We discovered that subfamilies of transposable elements are a major constituent of the hypomethylated landscape of tissue-Treg cells. Based on DNA hypomethylation homologies, our data unveil that the population of blood CCR8+ Treg cells contains recirculating human skin Treg cells. Our findings provide novel insights into the biology of human tissue-Treg cells, which are essential to harness these cells for therapeutic purposes. This GEO record comprises the whole-geome bisulfite sequencing data used in the study.

2025-05-20 | GSE286948 | GEO

Recirculating regulatory T cells mediate thymic regeneration [visium]

Project description:Recirculating regulatory T cells mediate thymic regeneration [visium]

2025-02-05 | GSE244641 | GEO

Recirculating regulatory T cells mediate thymic regeneration [single cell]

Project description:Recirculating regulatory T cells mediate thymic regeneration [single cell]

2025-02-05 | GSE244673 | GEO

recirculating aquaculture system

Project description:recirculating aquaculture system Raw sequence reads

| PRJNA555801 | ENA

Recirculating Aquaculture System Biofilters

Project description:Coldwater Recirculating Aquaculture System Biofilter Microbiomes

| PRJNA723328 | ENA

Recirculating juvenile seabass aquaculture

Project description:Recirculating juvenile seabass aquaculture Targeted loci environmental

| PRJNA513031 | ENA

Local DNA hypomethylation activates genes in rice endosperm

Project description:Cytosine methylation silences transposable elements in plants, vertebrates and fungi, but also regulates gene expression1. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C or T) and CHH, with CHH methylation targeted by the RNA interference (RNAi) pathway2. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation3. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, while CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data demonstrate that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops. Keywords: Epigenetics Examination of DNA methylation in rice

2010-11-01 | E-GEOD-22591 | biostudies-arrayexpress

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

Project description:Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755

2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress

DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts

Project description:DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.

2019-11-20 | GSE122394 | GEO

UW-Milwaukee Recirculating Aquaculture System Samples

Project description:UW-Milwaukee Recirculating Aquaculture System Targeted loci environmental

| PRJNA491503 | ENA