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RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE174048 | GEO | 2022/07/07

REPOSITORIES: GEO

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RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

Project description:The Ten-eleven translocation (TET) family of dioxygenases can mediate cytosine demethylation by catalyzing the oxidation of 5-methylcytosine (5mC). TET-mediated DNA demethylation controls the proper differentiation of embryonic stem cells and TET proteins display functional redundancy during early gastrulation. However, it is unclear if TET proteins have functional significance in mammalian skeletal development. Here, we report that Tet deficiency in mesoderm mesenchymal stem cells results in severe defects of bone development. The existence of any single Tet gene allele can support early bone formation, suggesting a potential functional redundancy of TET proteins. Integrative analyses of RNA-seq, Whole Genome Bisulfite Sequencing (WGBS) and Assay for Transposase-Accessible Chromatin (ATAC-seq) demonstrate that TET-mediated demethylation increases the chromatin accessibility of target genes by RUNX2 and facilities RUNX2-regulated transcription. In addition, TET proteins interact with RUNX2 through their catalytic domain to regulate cytosine methylation around RUNX2 binding region. The catalytic domain is indispensable for TET proteins to regulate RUNX2 transcription activity on its target genes and to regulate bone development. These results demonstrate that TET proteins function redundantly to regulate RUNX2 activity via dual mechanisms and maintain skeletal homeostasis.

2022-07-07 | GSE189655 | GEO

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS)

2022-07-07 | GSE174047 | GEO

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (ATAC-Seq)

2022-07-07 | GSE174045 | GEO

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (RNA-Seq)

2022-07-07 | GSE174046 | GEO

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

| PRJNA784093 | ENA

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS)

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS)

| PRJNA728061 | ENA

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development

| PRJNA728056 | ENA

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (ATAC-Seq)

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (ATAC-Seq)

| PRJNA728058 | ENA

RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (RNA-Seq)

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (RNA-Seq)

| PRJNA728060 | ENA

Detecting Differential Transcription Factor Activity from ATAC-Seq Data.

Project description:Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.

| S-EPMC6099720 | biostudies-literature

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