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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zepeda-Mendoza CJ,Mukhopadhyay S,Wong ES,Harder N,Splinter E,de Wit E,Eckersley-Maslin MA,Ried T,Eils R,Rohr K,Mills A,de Laat W,Flicek P,Sengupta AM,Spector DLdoi
10.1186/s12864-015-2137-5subject
Has Abstractpub_date
2015-11-21 00:00:00pages
982issn
1471-2164pii
10.1186/s12864-015-2137-5journal_volume
16pub_type
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