Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.
نویسندگان
چکیده
A three-dimensional chromatin state underpins the structural and functional basis of the genome by bringing regulatory elements and genes into close spatial proximity to ensure proper, cell-type-specific gene expression profiles. Here, we performed Hi-C chromosome conformation capture sequencing to investigate how three-dimensional chromatin organization is disrupted in the context of copy-number variation, long-range epigenetic remodeling, and atypical gene expression programs in prostate cancer. We find that cancer cells retain the ability to segment their genomes into megabase-sized topologically associated domains (TADs); however, these domains are generally smaller due to establishment of additional domain boundaries. Interestingly, a large proportion of the new cancer-specific domain boundaries occur at regions that display copy-number variation. Notably, a common deletion on 17p13.1 in prostate cancer spanning the TP53 tumor suppressor locus results in bifurcation of a single TAD into two distinct smaller TADs. Change in domain structure is also accompanied by novel cancer-specific chromatin interactions within the TADs that are enriched at regulatory elements such as enhancers, promoters, and insulators, and associated with alterations in gene expression. We also show that differential chromatin interactions across regulatory regions occur within long-range epigenetically activated or silenced regions of concordant gene activation or repression in prostate cancer. Finally, we present a novel visualization tool that enables integrated exploration of Hi-C interaction data, the transcriptome, and epigenome. This study provides new insights into the relationship between long-range epigenetic and genomic dysregulation and changes in higher-order chromatin interactions in cancer.
منابع مشابه
Liquid Biopsy as a Minimally Invasive Source of Thyroid Cancer Genetic and Epigenetic Alterations
In the blood of cancer patients, some nucleic acid fragments and tumor cells can be found that make it possible to trace tumor changes through a simple blood test called “liquid biopsy”. The main components of liquid biopsy are fragments of DNA and RNA shed by tumors into the bloodstream and circulate freely( ctDNAs and ctRNAs). tumor cells which are shed into the blood (circulating tumor cells...
متن کاملA Review of Driver Genetic Alterations in Thyroid Cancers
Thyroid cancer is a frequent endocrine related malignancy with continuous increasing incidence. There has been moving development in understanding its molecular pathogenesis recently mainly through the explanation of the original role of several key signaling pathways and related molecular distributors. Central to these mechanisms are the genetic and epigenetic alterations in these pathways, su...
متن کاملتغییرات ژنتیکی و اپیژنتیکی در سرطان تیرویید: مقاله مروری
Thyroid cancer is one of the most common endocrine malignancies and in the last two decades the number of involved people in the world has been increased. Thyroid cancer in Iran is the seventh most common cancer in women and 14th in men. In recent years many achievements regarding to molecular pathogenic factors such as the substantial role of signaling pathways and molecular abnormalities have...
متن کاملThe role of exosomes contents on genetic and epigenetic alterations of recipient cancer cells
Exosomes, as a mediator of cell-to-cell transfer of genetic information, act an important role in intercommunication between tumor cells and their niche including fibroblasts, endothelial cells, adipocytes and monocytes. Several studies have shown that tumor cells can influence their neighboring cells by releasing exosomes. These exosomes provide signaling cues for stimulation, activation, prol...
متن کاملGenetic and Epigenetic of Medullary Thyroid Cancer
Medullary thyroid carcinoma (MTC) is an infrequent calcitonin-producing neuroendocrine tumor that initiates from the parafollicular C cells of the thyroid gland. Several genetic and epigenetic alterations are collaterally responsible for medullary thyroid carcinogenesis. In this review article, we shed light on all the genetic and epigenetic hallmarks of MTC. From the genetic perspective, RET, ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Genome research
دوره 26 6 شماره
صفحات -
تاریخ انتشار 2016