Transcriptomics

Dataset Information

240

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


ABSTRACT: 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 signalling. 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. Hi-C experiments were conducted in MCF-7 and MCF-10A parental cells. The RNA-seq data associated with this study is deposited under the GEO accession number GSE71862.

ORGANISM(S): Homo sapiens  

SUBMITTER: Rachel P McCord   Gillian Browne  Ahmet R Barutcu  Gary S. Stein  Jane B Lian  Janet L Stein  Coralee E Tye  Terri L Messier  Andre J van wijnen  Bryan R Lajoie  AnthonyTerri N Imbalzano  Deli Hong  Gary S Stein  Job Dekker 

PROVIDER: E-GEOD-66733 | ArrayExpress | 2015-09-02

SECONDARY ACCESSION(S): SRP056040GSE66733PRJNA277846

REPOSITORIES: GEO, ArrayExpress, ENA

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