Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

ABSTRACT: Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

PROVIDER: PRJNA704985 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13786472_1.fastq.gz	Fastqsanger.gz
	SRR13786472_2.fastq.gz	Fastqsanger.gz
	SRR13786473_1.fastq.gz	Fastqsanger.gz
	SRR13786473_2.fastq.gz	Fastqsanger.gz
	SRR13786474_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 58

Similar Datasets

Comparative 3D Genome Architecture in Vertebrates

Project description:Comparative 3D Genome Architecture in Vertebrates

| PRJNA704983 | ENA

Comparative 3D Genome Architecture in Vertebrates (Hi-C)

Project description:Comparative 3D Genome Architecture in Vertebrates (Hi-C)

| PRJNA704984 | ENA

Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Project description:Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.

2022-04-12 | GSE167580 | GEO

Comparative 3D Genome Architecture in Vertebrates (Hi-C)

2022-04-12 | GSE167579 | GEO

Comparative 3D Genome Architecture in Vertebrates

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

2022-04-12 | GSE167581 | GEO

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States.

Project description:Epigenomic analysis of naïve human embryonic stem cells including histone modificatinos and 3D genomic architecture

2019-01-31 | GSE90680 | GEO

Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications

Project description:4C-seq experiments to study the evolution of the chromatin architecture of ancient gene regulatory blocks at the origin of vertebrates.

2021-03-23 | GSE136554 | GEO

SATB2 organizes the 3D genome architecture of cognition in cortical neurons [RNA-Seq]

Project description:SATB2 organizes the 3D genome architecture of cognition in cortical neurons [RNA-Seq]

| PRJNA1022069 | ENA

SATB2 organizes the 3D genome architecture of cognition in cortical neurons

Project description:SATB2 organizes the 3D genome architecture of cognition in cortical neurons

| PRJNA922863 | ENA

Comparative 3D genome analysis between neural retina and RPE reveals differential cis-regulatory interactions at retinal disease loci [UMI4C]

Project description:Vision depends on the functional interplay between the photoreceptor cells of the neural retina and the supporting cells of the underlying retinal pigment epithelium (RPE). Many genes involved in inherited retinal diseases (IRD) display highly specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. To understand the role of differential chromatin architecture in establishing tissue-specific expression patterns at IRD loci in the human neural retina and the RPE, we mapped genome-wide chromatin interactions by applying in situ Hi-C and H3K4me3 HiChIP to human adult post-mortem donor retinas. A comparative 3D genome analysis between neural retina and RPE revealed that almost 60% of known IRD genes were marked by differential cis-regulatory interactions or 3D genome structure. Furthermore, we zoomed in on tissue-specific chromatin interactions at the ABCA4 locus, which is implicated in the most common autosomal recessive IRD. We constructed high-resolution ABCA4 interaction profiles using UMI-4C, which, upon integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish, revealed tissue-specific CREs for ABCA4. In summary, through extensive comparative 3D genome mapping, based on genome-wide (Hi-C), promoter-centric (HiChIP) and locus-specific (UMI-4C) assays of human neural retina and RPE, we have shown that gene regulation at key IRD loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for genomic variation underlying unsolved IRD.

2024-04-08 | GSE235728 | GEO

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