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Title: Quantitative analysis of chromatin interactions upon copy number variation at mouse 4E2 [4C-seq]      
dateReleased:
07-03-2016
description:
The three-dimensional organization of chromatin has a critical impact on the regulation of gene expression. However, little is known about the effect of DNA copy number variants (CNVs) on chromatin organization. We performed an allele-specific chromatin conformation and gene expression analysis of wild-type (WT) mouse chromosome 4 and an engineered 4.3Mb chromosome 4 deletion in mouse embryonic fibroblasts. A newly developed quantitative framework for the analysis of paired-end 4C-seq data revealed a number of significant differentially interacting regions (DIRs) and higher-order chromatin compaction changes present in the deletion chromosome. Selected DIRs were validated by 3D DNA FISH experiments. We discovered a significant enrichment of CTCF and Smc1 binding sites within DIRs, as well as differentially expressed genes determined by RNA-Seq. Together, our findings highlight the complex effects of a 4E2 CNV on chromatin structure and function, both locally in the deletion chromosome and globally in the WT copy. Examination of chromatin contacts and gene expression in wild type chromosome 4 and a 4.3Mb deletion in chromosome 4 in mouse
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-64358
refinement:
raw
alternateIdentifiers:
64358
keywords:
functional genomics
dateModified:
12-28-2016
availability:
available
types:
gene expression
name:
Mus musculus
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-64358/E-GEOD-64358.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-64358/E-GEOD-64358.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64358
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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