Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation

ABSTRACT: Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation

PROVIDER: PRJNA994501 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25266162_1.fastq.gz	Fastqsanger.gz
	SRR25266162_2.fastq.gz	Fastqsanger.gz
	SRR25266163_1.fastq.gz	Fastqsanger.gz
	SRR25266163_2.fastq.gz	Fastqsanger.gz
	SRR25266164_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

2024-03-20 | GSE237268 | GEO

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

| PRJNA994504 | ENA

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (RNA-Seq)

Project description:Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (RNA-Seq)

| PRJNA994507 | ENA

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (RNA-Seq)

2024-03-20 | GSE237269 | GEO

Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation

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

2024-03-20 | GSE237271 | GEO

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Project description:Heterochromatin remodeling is critical for various cell processes. In particular, the “loss of heterochromatin” phenotype in cellular senescence engages with the progress of aging and age-related disorders. Although biological processes of senescent cells including senescence-associated heterochromatin foci (SAHF) formation, chromosome compaction and entry into senescence have been closely associated with high-order chromatin structure. the relationship between the high-order chromatin organization and the loss of heterochromatin phenotype during senescence has not been fully understood. By using senescent and late senescent fibroblasts induced by DNA damage harboring the “loss of heterochromatin” phenotype, we observed progressive 3D reorganization of heterochromatin during senescence. Facultative and constitutive heterochromatin marked by H3K27me3 and H3K9me3, respectively, showed different alterations. Facultative heterochromatin tends to switch from the repressive B-compartment to the active A-compartment, whereas constitutive heterochromatin shows no significant changes at the compartment level but enhanced interactions between themselves. Interestingly, both types show increased chromatin accessibility and gene expression leakage during senescence. Furthermore, increased chromatin accessibility in potential CTCF binding sites accompanies by the establishment of novel loops in constitutive heterochromatin. Finally, we also observed aberrant expression of repetitive elements, including LTR (long terminal repeat) and satellite classes. Overall, facultative and constitutive heterochromatin show multiscale but distinct alterations in the 3D map, meanwhile they also share the same features of increased chromatin accessibility and gene expression leakage. This study provides an epigenomic map of heterochromatin reorganization during senescence.

2019-12-31 | GSE133292 | GEO

Cellular rejuvenation protects neurons from inflammation mediated cell death (ATAC-seq).

Project description:Cellular rejuvenation protects neurons from inflammation mediated cell death (ATAC-seq).

| PRJNA1034145 | ENA

Cellular rejuvenation protects neurons from inflammation mediated cell death (RNA-seq).

Project description:Cellular rejuvenation protects neurons from inflammation mediated cell death (RNA-seq).

| PRJNA1036568 | ENA

DOT1L regulates chromatin reorganization and gene expression during sperm differentiation

Project description:Spermatozoa have a unique genome organization: their chromatin is almost completely devoid of histones and is formed instead of protamines which confer a high level of compaction and preserve paternal genome integrity until fertilization. Histone-to-protamine transition takes place in spermatids and is indispensable for the production of functional sperm. Here we show that the H3K79-methyltransferase DOT1L controls spermatid chromatin remodelling and subsequent reorganization and compaction of spermatozoon genome. Using a mouse model in which Dot1l is knocked-out (KO) in postnatal male germ cells, we found that Dot1l-KO sperm chromatin is less compact and has an abnormal content, characterized by the presence of transition proteins, immature protamine 2 forms and a higher level of histones. Proteomics and transcriptomics analyses performed on spermatids reveal that Dot1l-KO modifies the chromatin prior to histone removal, and leads to the deregulation of genes involved in flagellum formation and apoptosis during spermatid differentiation. As a consequence of these chromatin and gene expression defects, Dot1l-KO spermatozoa have less compact heads and are less motile, which results in impaired fertility.

2023-03-30 | PXD030734 | Pride

Microarray data for rejuvenation experiments through reprogramming

Project description:Proliferative and replicative senescent fibroblasts from aged human donors were reprogrammed towards pluripotency and re-differentiated in fibroblasts and then further analyzed for rejuvenation assessment. Comparison of microarrays were performed by non hierarchical clustering visualized in with Treeview software

2011-12-14 | E-GEOD-27924 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data