Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

ABSTRACT: Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

ORGANISM(S): Mus musculus

PROVIDER: GSE124205 | GEO | 2020/03/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains II (re-analysis)

Project description:Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

2020-03-27 | GSE97092 | GEO

The development and application of LIMe-Hi-C to simultanteously study lamina association, DNA methylation and chromosome conformation at baseline and upon EZH2 and DNMT1 inhibition

Project description:We developed and performed LIMe-Hi-C in order to assess lamina association, DNA methylation, and chromosome conformation in one experimental workflow. We combined LIMe-Hi-C with chemcial inhibition of EZH2 and DNMT1 to better understand the influence of H3K27me3 and DNA methylation on 3D genome organization.

2022-06-17 | GSE180228 | GEO

4C-seq: Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

Project description:Hox genes are essential regulators of embryonic development. They are activated in a temporal sequence following their topological order within their genomic clusters. Subsequently, states of activity are fine-tuned and maintained to translate into domains of progressively overlapping gene products. While the mechanisms underlying such temporal and spatial progressions begin to be understood, many of their aspects remain unclear. We have systematically analyzed the 3D chromatin organization of Hox clusters in vivo, during their activation using high-resolution circular chromosome conformation capture (4C-seq). Initially, Hox clusters are organized as single 3D chromatin compartments decorated with bivalent chromatin marks. Their progressive transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch one after the other, from an inactive to an active 3D compartment. These local 3D dynamics occur within a larger constitutive framework of interactions within the surrounding Topological Associated Domains, which confirms previous results that regulation of this process in primarily cluster intrinsic. The local step-wise progression in time can be stopped and memorized at various body levels and hence it may accounts for the various chromatin architectures previously described at different anterior to posterior body levels for the same embryo at a later stage. Circular Chromosome Conformation Capture (4C-seq) samples from mouse ES cells and mouse embryonic samples at different stages of development. Data based on 41 biological samples.

2014-04-28 | E-GEOD-55342 | biostudies-arrayexpress

Genome-wide maps of nuclear lamina interactions in single human cells. (Hi-C, KBM7 haploid)

Project description:Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization. Hi-C Data

2015-09-24 | E-GEOD-69841 | biostudies-arrayexpress

Gene regulatory loops at lamina-associated domains

Project description:The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are repressed, approximately ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to contact regulatory elements in LADs or outside LADs remains unclear. Here, we integrate transcriptomic, chromatin states, microscopy and publicly available enhancer-capture Hi-C data to show that expressed genes in LADs are able to connect to enhancers in LADs and inter-LADs. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with transcriptional regulation in this dynamic nuclear compartment.

2023-01-01 | GSE221288 | GEO

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription. Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome

2011-06-24 | E-GEOD-29509 | biostudies-arrayexpress

TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [H3K9me3 ChIP-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 | GSE143886 | GEO

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

2020-06-24 | GSE134623 | GEO

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

2020-06-24 | GSE134622 | GEO

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

2020-06-24 | GSE134621 | GEO