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3D Genome Engineering: Current Advances and Therapeutic Opportunities in Human Diseases [PDF]

Research
Dynamic chromatin 3-dimensional (3D) conformation is a key mechanism regulating gene expression and cellular function during development and disease.
Xing Jiang, Xiaoli Wang, Song Shen, Shangguo Hou, Chen Yu   +4 more
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Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC [PDF]

npj Digital Medicine
Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy associated with single-nucleotide variants in VHL, PBRM1, and SETD2. However, the role of structural variation (SV)—which have broader genomic impacts—and 3D genome architecture in ccRCC
Yu Dong, Wenjiao Xia, Zitong Yang, Liangliang Ren, Hongru Wang, Yiyang Zhou, Qinchen Li, Zhi Chen, Zhinan Xia, Yichun Zheng, Feifan Wang, Ning He, Bing Cheng, Dongmei Ma, Wei Shao, Wei Guo, Shuwen Wang, Ziqiao Liu, Junxiao Shen, Yiming Qi, Xuke Gong, Juan Jin, Bo Xie, Guixin Zhu, Cheng Zhang   +24 more
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Mapping the 3D genome architecture [PDF]

Computational and Structural Biotechnology Journal
The spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed ...
Ghazaleh Tavallaee, Elias Orouji
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Excessive DNA Double‐Strand Breaks–Associated 3D Genome Reorganization Contributes to Neural Tube Defects with Folate Deficiency [PDF]

Advanced Science
Neural tube defects (NTDs) are one of the most common congenital malformations. Folic acid deficiency in pregnant women increases the risk of developing NTDs; however, the underlying etiology and mechanisms remain elusive.
Ting Zhang, Lin Lin, Jianting Li, Caihua Li, Shengjun Liang, Xuemei Bai, Fang Wang, Yihua Bao, Dan Guo, Xiaochen Bo, Hao Li, Hebing Chen, Qiu Xie   +12 more
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Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens

Microbiology Spectrum, 2022
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi.
Chongjing Xia, Liang Huang, Jie Huang, Hao Zhang, Ying Huang, Moussa Benhamed, Meinan Wang, Xianming Chen, Min Zhang, Taiguo Liu, Wanquan Chen   +10 more
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Modeling the 3D genome of plants

Nucleus, 2021
Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the ...
Marco Di Stefano, Hans-Wilhelm Nützmann
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Three-dimensional chromatin architecture in plants – General features and novelties

European Journal of Cell Biology, 2023
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades.
Edouard Tourdot, Stefan Grob
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3D genome organization

Scientific Reports, 2022
Our genomes are highly organized spatially in three-dimensions (3D). In interphase nuclei, the genome is anchored and regulated by various nuclear scaffolds and structures, including the nuclear lamina at the nuclear edge, and nucleoli located more ...
Asli Silahtaroglu, Joanna M. Bridger, Elissa P. Lei   +2 more
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Novel biological insights revealed from the investigation of multiscale genome architecture

Computational and Structural Biotechnology Journal, 2023
Gene expression and cell fate determination require precise and coordinated epigenetic regulation. The complex three-dimensional (3D) genome organization plays a critical role in transcription in myriad biological processes. A wide range of architectural
Tianyi Ding, He Zhang
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DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

Cell Reports, 2021
Summary: DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects ...
Qian Du, Grady C. Smith, Phuc Loi Luu, James M. Ferguson, Nicola J. Armstrong, C. Elizabeth Caldon, Elyssa M. Campbell, Shalima S. Nair, Elena Zotenko, Cathryn M. Gould, Michael Buckley, Kee-Ming Chia, Neil Portman, Elgene Lim, Dominik Kaczorowski, Chia-Ling Chan, Kirston Barton, Ira W. Deveson, Martin A. Smith, Joseph E. Powell, Ksenia Skvortsova, Clare Stirzaker, Joanna Achinger-Kawecka, Susan J. Clark   +23 more
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