Dataset Information
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
Ontology highlight
ABSTRACT: Background
Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2.Results
A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed.Conclusions
Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function.
SUBMITTER: Zepeda-Mendoza CJ
PROVIDER: S-EPMC4654810 | biostudies-literature | 2015 Nov
REPOSITORIES: biostudies-literature
Publications
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.
BMC genomics 20151121
<h4>Background</h4>Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2.<h4>Results</h4>A significant number of differ ...[more]
