Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

ABSTRACT: The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identified de novo cell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization. Here we submit our bulk RNA-sequencing data on E14.5 mouse fetal liver, used in the study to validate image-based RNA profiling results.

ORGANISM(S): Mus musculus

PROVIDER: GSE148072 | GEO | 2020/05/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [DamID and ChIP]

Project description:Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. Our studies describe fundamental principles of how the architectural proteins contribute to genome folding at multiple genomic scales and transcriptional regulation.

2021-09-16 | GSE183958 | GEO

Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [pA-DamID]

2021-09-16 | GSE181693 | GEO

Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [RNA-seq]

2022-08-11 | GSE181849 | GEO

Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [ChIP-seq]

2022-08-11 | GSE181847 | GEO

Rapid depletion of the cohesin subunits and CTCF reveals their role in maintaining high-order genome architecture [ATAC-seq]

2022-08-11 | GSE181846 | GEO

Chromosomal Architecture of Arabidopsis and its Implication in Transposon Intergration

Project description:Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus. HiC experiments were performed on Arabidopsis thaliana Col-0 wildtype, homozygous crwn1-1, and homozygous crwn4-1 14-day-old seedlings

2014-08-18 | E-GEOD-55960 | biostudies-arrayexpress

TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [ATAC-seq]

Project description:Within mammalian nuclear space, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs), associated with transcriptional repression. However, the molecular mechanisms underlying these 3D chromatin architectures remain undeciphered. Here, we demonstrate the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. Topors knockdown in mouse hepatocytes results in cell proliferation and migration promotion, as well as arrest in the S phase of the cell cycle. RNA-seq analysis shows that 373 genes are up-regulated, some of which are associated with nuclear structure, and 316 genes exhibit down-regulated, many related to metabolic process. Chromatin accessibility is inclined to alter in the intergenic regions, including enhancers. Chromatin-lamina interactions decrease globally, and the coverage of LADs reduces from 53.31% to 46.52%. Furthermore, Topors knockdown leads to significantly increasing interactions between A and B compartments in cis and in trans. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. Collectively, our data reveal that TOPORS functions as a regulator in chromosome folding, providing novel insights into the architectural role of tumor suppressors in higher-order genome organization.

2020-06-24 | GSE134619 | GEO

TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [H3K9me3 ChIP-seq]

2020-06-24 | GSE143886 | GEO

TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [DamID]

2020-06-24 | GSE133224 | GEO

TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [RNA-seq]

2020-06-24 | GSE134623 | GEO