Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cellular reprogramming is driven by widespread rewiring of promote-enhancer interactions

ABSTRACT: Interactions between promoters and cis-regulatory elements, such as enhancers, play a role in gene regulation. However, the role of three-dimensional (3D) chromatin structure in orchestrating changes in transcription during cell fate transition is not fully understood. Here, we performed integrated analyses of chromosomal architecture, epigenetics and gene expression using Hi-C, promoter Capture Hi-C (PCHi-C), ChIP sequencing, and RNA sequencing during trans-differentiation of preB cells into macrophages with a β-estradiol inducible CEBPα-ER transgene. Within 1 hour of β-estradiol induction, CEBPα translocates from the cytoplasm to the nucleus and binds to thousands of promoters and putative regulatory elements, resulting in downregulation of preB cell specific genes and induction of macrophage specific genes. Hi-C results were remarkably consistent throughout transinduction, revealing only a small number of TAD boundary location changes, and A/B compartment switches despite changes in expression of thousands of genes. PCHi-C reveals changes in promoter-anchored loops with decrease in interactions parallel with their decreased expression, and new promoter-anchored interactions with macrophage specific genes concordant with their increased expression.Overall, our data demonstrate that CEBPα-induced transinduction involves few changes in genome architecture that are detectable by Hi-C, and widespread reorganization of thousands of promoter anchored loops with PCHi-C that drive changes in cell identity.

ORGANISM(S): Mus musculus

PROVIDER: GSE221737 | GEO | 2023/11/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology.

Project description:Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in inducible Pax7-expressing skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterized at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and differentiation. We identified key promoter-enhancer interaction motifs, namely, cliques and networks, and interactions that were dependent on Pax7 binding. Remarkably, we found that the majority of super-enhancers were bound by Pax7 and a cadre of associated factors that maintained an epigenetic memory of active enhancers in the absence of Pax7. Lastly, we identified a previously uncharacterized Pax7-bound enhancer hub that simultaneously regulates the essential myosin heavy chain cluster during skeletal muscle cell differentiation. Our studies lay the groundwork for understanding the three-dimensional conformation of chromatin in muscle stem cells.

2020-10-31 | GSE150638 | GEO

Promoter capture Hi-C of CD34+ haematopoietic stem cells

Project description:CD34+ heamatopoietic stem cells were isolated from the bone marrow of two healthy donors undergoing total hip replacement. Promoter capture Hi-C (PCHi-C) was performed on these cells using the protocol according to Mifsud et al. 2015, with the exception that ligation was performed in situ, and a slightly modified bait capture set was used. Bait positions in hg19 are included as an additional file.

2021-10-15 | E-MTAB-10701 | biostudies-arrayexpress

Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology

Project description:Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterized at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and differentiation. To further investigate transcriptional regulatory mechanisms governed by Pax7, we used immuno-affinity purification and mass spectrometric sequencing to identify the compendium of Pax7-associated proteins in muscle progenitors. Although Pax7-associated proteins have been identified in myoblasts, it is likely that such an approach would fail to uncover progenitor specific interactions with this protein. We therefore isolated chromatin from iPax7 cells engineered with a single, inducible copy of the Flag-tagged Pax7 transgene integrated next to the Hprt locus, which is expected to maintain expression levels comparable to those of satellite cells in the presence of Dox. Through purification of Flag-Pax7, we identified a cohort of factors and complexes involved in gene activation or repression and remodeling of chromatin and genome architecture that were substantially enriched compared to the uninduced control. We also identified a large cohort of sequence-specific TFs, including several that were shown to play an essential role in muscle stem cells (e.g., Foxk1, Six1, Runx1, Tead1, Nfix) and that are recruited to Pax7-bound enhancers in muscle cells. Importantly, we also confirmed multiple interactions from our proteomic screen through immunoprecipitation and western blotting.

2020-10-30 | MSV000086392 | MassIVE

The promoter interactome of cardiomyocytes differentiated from human embryonic stem cells links regulatory elements to cardiac gene promoters

Project description:Long-range chromosomal interaction is an important mechanism by which differentiating cells organise three dimensional promoter-enhancer networks to regulate lineage-specifying, developmental, regulatory genes1,2. Distal promoter contacts in pluripotent stem and specialised cell types, such as foetal liver cells, form co-regulated gene networks correlated with their biological functions1. Promoter interactomes of 17 primary blood cell types also reflect high cell-type specificity3. The lineage-specifying promoter interactions can be constrained by polycomb repressive complexes and genes with specialised functions will be selectively released from this poised network during cell fate specification or differentiation2. The cis-regulatory contact upon lineage commitment is also a dynamic process that includes acquisition and loss of specific promoter interactions4. We characterise 5126 promoter-enhancer interactions specific to cardiomyocytes differentiated from human embryonic stem cells (hESC-CM) by performing a differential promoter capture Hi-C (PCHi-C)5 approach that allows physical promoter-enhancer contacts in hESC-CM to be identified against the background level of embryonic stem cells’ interactions. This approach enables us to extract key genomic regulators and their target genes highly specific to the cardiovascular development and functions.

2018-07-15 | GSE100720 | GEO

Chromosome contacts in activated T cells identify autoimmune disease-candidate genes

Project description:Autoimmune disease-associated DNA variants are preferentially found in regions with putative regulatory function in immune cells, particularly CD4+ T cells. Linking such regulatory elements to gene promoters in disease-relevant cells and contexts is essential to identify disease candidate genes. Here we show that the activation of CD4+ T cells invokes changes in the activity of regulatory elements and transcription of RNAs that correspond to changes in the expression of their interacting genes identified by promoter capture Hi-C (PCHi-C).

| EGAS00001001961 | EGA

Promoter Capture Hi-C of mouse ESC and TSC

Project description:Chromatin organisation of trophoblast stem cells (TSC) were compared with that of embryonic stem cells (ESC). The method enriches Hi-C libraries, to detect promoter interactions at restriction fragment level. We prepared Hi-C libraries from TSC and ESC (serum grown) samples and enriched them with a promoter capture bait system that captures ~22.000 promoters. Promoter interactions were then analysed using the GOTHiC pipeline.

2018-09-05 | E-MTAB-6585 | biostudies-arrayexpress

Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation

Project description:Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter anchored chromatin loops within four hours after induction of differentiation of 3T3-L1 preadipocytes. This reorganization is tightly coupled to dynamic changes in target gene expression. The formation of promoter-enhancer loops is tightly linked to the activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1 and P300 proteins to these regions. Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.

2017-04-26 | GSE95533 | GEO

HiCAR analysis of human embryonic stem cell differentiation reveals principles of cis-regulatory chromatin reorganization controlling developmental gene expression

Project description:we report a novel method, Hi-C on Accessible Regulatory DNA (HiCAR), which leverages principles of ATAC-seq and high-throughput 3C-assay for genome-wide profiling of chromatin accessibility and open chromatin anchored cRE interactions.

2022-02-28 | GSE162819 | GEO

Promoter capture GM12878 CD34

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC lib

2015-03-01 | E-MTAB-2323 | biostudies-arrayexpress

Promoter Capture-HiC in Ring1a KO and Ring1a/b dKO mouse ES cells

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts mediated by the PRC1 complex we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC library in Ring1a KO and Ring1a/b dKO mouse ES cells.

2015-08-01 | E-MTAB-3109 | 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