Alterations in three-dimensional organization of the cancer genome and epigenome

7Citations
Citations of this article
44Readers
Mendeley users who have this article in their library.

Abstract

The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome. Notably, we find that additional topologically associated domain (TAD) boundaries are formed in cancer cells resulting in smaller TADs and altered gene expression profiles. The new TAD boundaries are commonly associated with copynumber changes observed in the cancer genome.We also identified new cancer-specific chromatin loops within TADs that are enriched for enhancers and promoters. Finally, we find that many of the long-range epigenetically silenced (LRES) and longrange epigenetically active (LREA) regions in cancer are characterized by differential chromatin interactions. Together our data provide a new insight into charting alterations in higher-order structure and the relationship with genetic, epigenetic, and transcriptional changes across the cancer genome.

Cite

CITATION STYLE

APA

Achinger-Kawecka, J., Taberlay, P. C., & Clark, S. J. (2016). Alterations in three-dimensional organization of the cancer genome and epigenome. Cold Spring Harbor Symposia on Quantitative Biology, 81(1), 41–51. https://doi.org/10.1101/sqb.2016.81.031013

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free