Three-Dimensional Genomics: A New Perspective and Therapeutic Strategies in Prostate Cancer Research
DOI:
https://doi.org/10.62051/5arw4d68Keywords:
Three-dimensional genomics; Prostate cancer; Chromatin structure.Abstract
Prostate cancer (PC) poses significant health risks to men globally. Enhancing our understanding of prostate cancer biology is crucial for facilitating early diagnosis and effective treatment strategies. A multitude of high-throughput sequencing studies, encompassing whole genome resequencing, transcriptome sequencing, and genome-wide association studies, have unearthed vital point mutations, structural variations, and epigenomic alterations linked to prostate cancer. These findings have significantly enriched our knowledge of the genomic framework for prostate cancer. Still, these investigations have predominantly centered on the one- or two-dimensional landscape of the genome. Research in three-dimensional genomics underscores the critical role of the genome's three-dimensional spatial structure in maintaining normal cellular functions. Additionally, it demonstrates that dysregulation of key genes in numerous cancers relates to the chromatin's spatial organization across various levels. This article explores the intricate three-dimensional architecture of chromosomes. It outlines the progressive development of techniques used in three-dimensional genomic research and synthesizes the application of these techniques in the study of prostate cancer biology. Furthermore, it proposes potential therapeutic strategies for prostate cancer.
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References
Watson J D, Crick F H C. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid [J]. Nature, 1953, 171 (4356): 737 - 738.
Huang Q, Li Q, Zhang Y. Linking chromatin conformation to gene function [J]. Hereditas, 2020, 42 (01): 1 - 17.
Cremer T, Cremer M. Chromosome territories [J]. Cold Spring Harbor perspectives in biology, 2010, 2 (3): a003889.
Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells [J]. Nature reviews genetics, 2001, 2 (4): 292 - 301.
Bolzer A, Kreth G, Solovei I, et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes [J]. PLoS biology, 2005, 3 (5): e157.
Lieberman-Aiden E, Van Berkum N L, Williams L, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome [J]. science, 2009, 326 (5950): 289 - 293.
Rao S S P, Huntley M H, Durand N C, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping [J]. Cell, 2014, 159 (7): 1665 - 1680.
Du Z, Zheng H, Huang B, et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development [J]. Nature, 2017, 547 (7662): 232 - 235.
Tena J J, Santos-Pereira J M. Topologically associating domains and regulatory landscapes in development, evolution and disease [J]. Frontiers in cell and developmental biology, 2021, 9: 702787.
Bonev B, Cavalli G. Organization and function of the 3D genome [J]. Nature Reviews Genetics, 2016, 17 (11): 661 - 678.
Markenscoff-Papadimitriou E, Allen W E, Colquitt B M, et al. Enhancer interaction networks as a means for singular olfactory receptor expression [J]. Cell, 2014, 159 (3): 543 - 557.
Fullwood M J, Liu M H, Pan Y F, et al. An oestrogen-receptor-α-bound human chromatin interactome [J]. Nature, 2009, 462 (7269): 58 - 64.
] Mumbach M R, Rubin A J, Flynn R A, et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture[J]. Nature methods, 2016, 13 (11): 919 - 922.
Yuan J, Houlahan K E, Ramanand S G, et al. Prostate Cancer transcriptomic regulation by the interplay of germline risk alleles, somatic mutations, and 3D genomic architecture [J]. Cancer discovery, 2022, 12 (12): 2838 - 2855.
Corces M R, Corces V G. The three-dimensional cancer genome[J]. Current opinion in genetics & development, 2016, 36: 1 - 7.
Taberlay P C, Achinger-Kawecka J, Lun A T L, et al. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations [J]. Genome research, 2016, 26 (6): 719 - 731.
Hsieh C L, Fei T, Chen Y, et al. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation [J]. Proceedings of the National Academy of Sciences, 2014, 111 (20): 7319 - 7324.
Guo Y, Perez A A, Hazelett D J, et al. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops [J]. Genome biology, 2018, 19: 1 - 17.
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