Dataset Information
Chromosome interaction copy number analysis of mouse neonatal liver cells, and undifferentiated and differentiated embryonic stem cells using circular chromosome conformation capture (4C) assays
Ontology highlight
ABSTRACT:
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/
INSTRUMENT(S): ScanArray 4000 [PerkinElmer]
ORGANISM(S): Mus musculus
SUBMITTER: gholamreza tavooisdana
PROVIDER: E-MEXP-870 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.
Nature genetics 20061008 11
Accumulating evidence converges on the possibility that chromosomes interact with each other to regulate transcription in trans. To systematically explore the epigenetic dimension of such interactions, we devised a strategy termed circular chromosome conformation capture (4C). This approach involves a circularization step that enables high-throughput screening of physical interactions between chromosomes without a preconceived idea of the interacting partners. Here we identify 114 unique sequenc ...[more]
