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The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [ChIRP-seq]

ABSTRACT: The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [ChIRP-seq]

PROVIDER: PRJNA848653 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23945424_1.fastq.gz	Fastqsanger.gz
	SRR23945424_2.fastq.gz	Fastqsanger.gz
	SRR23945425_1.fastq.gz	Fastqsanger.gz
	SRR23945425_2.fastq.gz	Fastqsanger.gz

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Similar Datasets

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [ChIRP-seq]

Project description:The transcription factor ΔNp63, a master regulator of epithelial biology, is involved in regulating epithelial stem cell function and maintaining the integrity of stratified epithelial tissues such as the epidermis. To this end, ΔNp63 acts as transcriptional repressor or activator towards a distinct subset of protein-coding genes and microRNAs. However, how and whether ∆Np63 regulates long non-coding RNA (lncRNAs) expression is not known. Here, we identified the lncRNAs NEAT1 and MALAT1 as a bona fide ΔNp63 transcriptional targets. We found that in proliferating human keratinocytes ∆Np63 represses NEAT1 and MALAT1 expression by recruiting the histone deacetylates HDAC1/HDAC2 to the p63 DNA binding site located in the proximal promoter of NEAT1 and MALAT1 genomic loci. Upon induction of differentiation, ∆Np63 down-regulation is associated by a marked increase of NEAT1 RNA levels, resulting in an increased assembly of paraspeckles foci both in vitro and in human skin tissues. RNA-seq analysis associated with global DNA binding profile (ChIRP-seq) revealed that NEAT1 associates with the promoter of key epithelial transcription factors sustaining their expression during epidermal differentiation. These molecular events might explain the inability of NEAT1-depleted keratinocytes to undergo the correct epidermal differentiation program. Remarkably, NEAT1 expression is dysregulated in those skin pathologies characterized by aberrant keratinocytes differentiation such as ichthyosis and psoriasis, suggesting its potential involvement in the pathogenesis of skin disorders.

2023-05-17 | GSE205959 | GEO

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [RNA-seq]

2023-05-17 | GSE205960 | GEO

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation

Project description:The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation

| PRJNA848649 | ENA

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [microarray]

Project description:The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [microarray]

| PRJNA973105 | ENA

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [RNA-seq]

Project description:The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [RNA-seq]

| PRJNA848654 | ENA

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation [microarray]

Project description:Profile of the genomic binding sites for endogenous NEAT1 in human primary keratinocytes (HEKn) maintanied for six days in high calcium-containing medium. Chromatin was isolated from gluteraldeyde-fixed nuclei of differentiated HEKn and NEAT1-associated D

2023-05-17 | GSE232654 | GEO

The long non-coding NEAT1 is a DNp63 target gene able to modulate epidermal differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-05-19 | GSE205961 | GEO

RNA-sequence analysis of mammary epithelial cells with and without DNp63 using tamoxifen driven conditional deletion of DNp63

Project description:Several genes involved in oxidative phosphorylation and stem cells and polarity were reduced in DNp63 floxed mice compared to WT

2022-09-05 | GSE137062 | GEO

Investigating the Role of DNp63 in breast cancer

Project description:The goal of this study was to characterize the differences in the global binding affinity of DNp63 to different genomic regions and its downstream target genes in human breast xenograft tumors.

2020-08-05 | GSE144995 | GEO

NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4

Project description:Long non-coding (lnc)RNA emerge as regulators of genome stability. The nuclear enriched abundant transcript 1 (NEAT1) locus encodes two lncRNA isoforms that modulate gene expression, growth and proliferation in mammals. Interestingly, NEAT1 transcripts are overexpressed in many tumours and induced by DNA damage, suggesting a genome-protective function. However, the precise role of NEAT1 in the DNA damage response (DDR) is unclear. Here, we investigate the expression, modification levels, localization and structure of NEAT1 in response to DNA double-strand breaks (DSBs) induced by the topoisomerase-II inhibitor etoposide or the locus-specific endonuclease AsiSI. We find that induction of DSBs increases both the levels and N6-methyladenosine (m6A) marks on NEAT1, which promotes alterations in NEAT1 secondary structure and accumulation of hyper-methylated NEAT1 at a subset of promoter-associated DSBs to facilitate efficient DSB signalling. The depletion of NEAT1, in turn, delays the response to DSBs and triggers elevated DNA damage. The genome-protective role of NEAT1 is mediated by the RNA methyltransferase 3 (METTL3) and involves spreading of the chromodomain helicase DNA binding protein 4 (CHD4) upon release from NEAT1. Together, we describe a novel RNA-dependent DDR pathway that couples NEAT1 to the recognition and repair of DSBs.

2024-09-17 | GSE256233 | GEO

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