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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.

cancer

Authors: A Rasim AR. Barutcu, Bryan R BR. Lajoie, Rachel P RP. McCord, Coralee E CE. Tye, Deli D. Hong, Terri L TL. Messier, Gillian G. Browne, Andre J AJ. van Wijnen, Jane B JB. Lian, Janet L JL. Stein, Job J. Dekker, Anthony N AN. Imbalzano, Gary S GS. Stein
Published: 09/28/2015, Genome biology

Background

Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines.

Results

Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells.

Conclusions

We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer.

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