Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE98194 | GEO | 2017/04/26

SECONDARY ACCESSION(S): PRJNA384226

REPOSITORIES: GEO

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Project description:Experimental design Using Circular chromosome conformation capture (4C) assay to uncovers epigenetically regulated intra- and inter-chromosomal interaction network To examine restrictions imposed by the nuclear structure on such cis/trans-chromosomal networks, we developed a high-throughput screening assay 4C and identified 114 different sequences from all autosomes in mouse liver cells. To check the relative frequencies of interactions, the 114 sequences were PCR amplified and spotted on glass to make dedicated microarray. The microarray and 3C validation showed that most of the sequences interact with primarily the maternally inherited H19 imprinting control region (ICR). The epigenetic feature of these interactions was highlighted by the observation that 19% of 4C library sequences are derived from 11 different imprinted domains. In some of these instances, differentially methylated regions (DMRs) interact both in cis and in trans. Moreover, the patterns of chromosomal interactions undergo reprogramming during in vitro maturation of embryonic stem cells. We propose that the nuclear organization of mammalian cells displays considerable plasticity to potentially throw new light on development, cancer epigenetics and evolution of imprinting. Key words: Chromosome conformation capture, CTCF, ICR(Imprinting Control Region) Experimental factors: Genetic variation Experimental design: The 4C samples from both neonatal liver cell SD7 x 142* and 142* x SD7; differentiated embryonic cells and undifferentiated embryonic cells were amplified, fluorescently labeled, and hybridized to 4C dedicated microarray. Quality control steps taken: using pooled samples and gDNA as input, about half of most frequently interactions were confirmed by replicates and dyes swaps. Processed data and a data transformation protocol can be download from ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-870/

Dataset Information

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

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