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Circularized chromosome conformation capture followed by sequencing (4C-seq) in A549 cell line

ABSTRACT: To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(T/T),A549(C/C).

ORGANISM(S): Homo sapiens

PROVIDER: GSE225518 | GEO | 2023/05/10

REPOSITORIES: GEO

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circularized chromosome conformation capture followed by sequencing (4C-seq) in the heterozygous (T/C) A549 cell line

Project description:To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(A/C).

2023-05-10 | GSE213196 | GEO

Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

Project description:We performed 4C-seq in the A549 cell line to investigate changes in chromatin interactions at the ZBTB16 locus. Cells were treated with either 100 nM dexamethasone or 0.1% ethanol. After 4 hours, cells were washed 2x with PBS and cultured in hormone-free medium for 24 hours, after which cells were treated again for 4 hours with either 100 nM dexamethasone or 0.1% ethanol. Experiments were performed in two biological replicates. For each treatment, 4C-seq data were generated for the following two viewpoints: ZBTB16 promoter-proximal viewpoint coordinates: chr11:113929670-113930464 (hg19) ZBTB16 intronic viewpoint coordinates: chr11:114051224-114051804 (hg19)

2021-05-03 | E-MTAB-9915 | biostudies-arrayexpress

Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GR

Project description:To investigate the interaction landscape at the GILZ locus we performed 4C-seq in A549 (ATCC CCL-185) and U2OS cells stably expressing rat GR (Rogatsky et al. , Mol Cell Biol, 1997. 17(6): p. 3181-93.) upon hormone treatment (1.5 h, 1 M dexamethasone). Experiments were performed in two biological replicates using hg19 chrX:106,960,488-106,960,865 as a viewpoint.

2018-04-12 | E-MTAB-5350 | biostudies-arrayexpress

Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

Project description:Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

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Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GRα

Project description:Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GRα

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Circularized Chromosome Conformation Capture (4C) for the genome-wide characterization of mammalian promoters with distal enhancer functions

Project description:We report the application of 4C technology for the identification of interaction points between the promoters of the RNF44 and FAF2 genes and their putative distal enhancers.

2017-04-26 | GSE98194 | GEO

Identification of p66Shc promoter interactional DNA fragments using Circularized Chromosome Conformation Capture coupled with next-generation sequencing (4C-seq)

Project description:p66Shc is encoded by the SHC1 gene, which contains two tandem promoters that generate three proteins (p46, p52 and p66). More recently, p66Shc was found to localize to focal adhesions that reports cell attachment and is required for anoikis through a RhoA-dependent mechanosensory test (Ma et al., J Cell Biol, 179, 23-31). Consistent with its role in anoikis, p66Shc is expressed in normal epithelial and endothelial cells but not in hematopoietic cells that survive in unanchored conditions. To uncover the epigenetic regulation mechanisms of p66Shc expression, here we performed 4C-seq assays with p66Shc promoter as a bait in HUVEC and U937 cells. Our results identify different p66Shc promoter interactional DNA fragments in different cell types.

2017-12-30 | GSE106449 | GEO

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture.

Project description:Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to 10-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes.

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Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

2020-10-01 | GSE121623 | GEO

Chromosome conformation capture-on-chip sequencing (4C) analysis of the FCGR2A promoter.

Project description:We performed 4C analysis of the immunity-related FCGR2A gene promoter in the U937 monocytic cell line, using cells in resting conditions. The FCGR2A transcription start site was used as bait.

2022-06-22 | GSE180154 | GEO

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