Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Charting the regulatory landscape of TP53 on transposable elements in cancer [WGBS]

ABSTRACT: Charting the regulatory landscape of TP53 on transposable elements in cancer [WGBS]

PROVIDER: PRJNA1090103 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28401039_1.fastq.gz	Fastqsanger.gz
	SRR28401039_2.fastq.gz	Fastqsanger.gz
	SRR28401040_1.fastq.gz	Fastqsanger.gz
	SRR28401040_2.fastq.gz	Fastqsanger.gz
	SRR28401041_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Charting the regulatory landscape of TP53 on transposable elements in cancer [ATAC-seq]

Project description:Charting the regulatory landscape of TP53 on transposable elements in cancer [ATAC-seq]

| PRJNA1090105 | ENA

Charting the regulatory landscape of TP53 on transposable elements in cancer [RNA-seq]

Project description:Charting the regulatory landscape of TP53 on transposable elements in cancer [RNA-seq]

| PRJNA1090101 | ENA

Charting the regulatory landscape of TP53 on transposable elements in cancer [ChIP-seq]

Project description:Charting the regulatory landscape of TP53 on transposable elements in cancer [ChIP-seq]

| PRJNA1090102 | ENA

Charting the regulatory landscape of TP53 on transposable elements in cancer [WGBS]

Project description:The relationship between p53 and transposable elements (TEs) has been obscure. Thus, comprehensive profiling of TE-derived transcripts dynamics under the regulation of p53 provides valuable resources for more clarity in p53’s roles in cancer. In this study, we created three cancer cell lines with p53 genetic status as the only variable and combined long-read RNA-seq and short-read RNA-seq to define TE and TE-derived transcripts’ regulatory dynamics. We identified in total 2,503 transcripts that use TE as potential promoters, among which, 141 to 210 are activated by p53. We found ERVs to be a main driver of potential promoters, followed by LINEs. Epigenomic profiling including chromatin accessibility and DNA methylation provided additional support for active promoter potential for p53 upregulated TE-derived transcripts. Short-term restoration of p53 partially recovered chronic p53-regulated TE-derived transcript profile but gain of function TP53 mutations, R175H and R273H, did not show evidence to act via TE network. Overall, we provide a controlled isogenic cancer cell line system with TP53 mutation status as the only genetic variable, deliver a high confidence TE and TE-derived transcript atlas and comprehensively identify active TE promoters that are direct and indirect targets of p53.

2024-10-20 | GSE262054 | GEO

Charting the regulatory landscape of TP53 on transposable elements in cancer [RNA-seq]

2024-10-20 | GSE262053 | GEO

Charting the regulatory landscape of TP53 on transposable elements in cancer [ChIP-seq]

2024-10-20 | GSE262052 | GEO

Charting the regulatory landscape of TP53 on transposable elements in cancer [ATAC-seq]

Project description:Comprehensive profiling of transposable element (TE)-derived transcripts dynamics under the regulation of p53 provides valuable resources for more clarity in p53 pleiotropic roles in cancer. In this project, we created three cancer cell lines with p53 genetic status as the only variable and used long-read RNA-seq to profile TE and TE-derived transcripts’ regulatory dynamics. By using both short-read RNA-seq and long-read RNA-seq, novel TE-derived transcripts as a function of p53 status were accurately profiled for the first time. We identified in total 2503 transcripts that use TE as potential promoters, among which, 141 to 210 are activated by p53 across three cancer cell lines. We found ERVs to serve as potential driving promoters, followed by LINEs. Epigenomic information from chromatin accessibility and DNA methylation provided additional support for active promoter potential for p53 upregulated TE-derived transcripts. Short-term restoration of p53 partially recovered chronic p53-regulated TE-derived transcriptional profile; whereas gain of function TP53 mutations, R175H and R273H, did not show evidence to act via TE network. Overall, in this paper, we provide a controlled isogenic cancer cell line system with TP53 mutation status as the only genetic variable, deliver a high confidence TE and TE-derived transcript atlas, and comprehensively identify active TE promoters that are direct and indirect targets of p53.

2024-10-20 | GSE262051 | GEO

TNRC18 recognizes H3K9me3 to mediate transposable elements silencing at ERV regions [WGBS]

Project description:TNRC18 recognizes H3K9me3 to mediate transposable elements silencing at ERV regions [WGBS]

| PRJNA978064 | ENA

Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease

Project description:Growing evidence implicates transposable elements (TEs) in aging and Alzheimer’s disease (AD). To evaluate potential transcriptional and epigenetic differences related to TE expression in this context, we generated whole blood total RNA-seq, and peripheral blood cell whole-genome bisulfite sequencing (WGBS), and transposase-accessible chromatin sequencing (ATAC-seq) on samples from healthy middle-aged/older adults, mild cognitive impairment (MCI), and AD patients.

2024-08-01 | GSE270454 | GEO

Transposable Elements in Frontotemporal Lobar Degeneration

Project description:Transposable Elements in Frontotemporal Lobar Degeneration

| PRJNA561865 | ENA