Article
Biochemical Research Methods
Jian Liu, Pingjing Li, Jialiang Sun, Jun Guo
Summary: With the development of the chromosome conformation capture technique, the study of genome spatial conformation based on the Hi-C technique has significantly advanced. Previous research has shown that genomes are folded into a hierarchy of 3D structures associated with topologically associating domains (TADs), and detecting TAD boundaries is crucial for analyzing the 3D genome architecture. This paper introduces a novel TAD identification method called LPAD, which extracts node correlations from chromosome interactions using the random walk with restart and builds an undirected graph from Hi-C contact matrix. LPAD utilizes label propagation to discover communities and generate TADs, demonstrating high accuracy in TAD detection compared to existing methods. Experimental evaluation also confirms LPAD's effectiveness in identifying TAD boundaries through enrichment of histone modifications.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Kun Liu, Hong-Dong Li, Yaohang Li, Jun Wang, Jianxin Wang
Summary: In this study, we conducted a systematic comparison of twenty-six TAD callers, evaluating their performance in terms of TAD continuity, quality, and assessment. By considering multiple criteria, we provided a concise, comprehensive, and systematic framework for the detection and evaluation of TADs.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Virology
Mel Campbell, Chanikarn Chantarasrivong, Yuichi Yanagihashi, Tomoki Inagaki, Ryan R. Davis, Kazushi Nakano, Ashish Kumar, Clifford G. Tepper, Yoshihiro Izumiya
Summary: This study reveals the 3D structure of the KSHV genome and presents a 3D genomic structural model for the virus. The KSHV genome exhibits similar structural features and undergoes reorganization during reactivation, facilitating viral gene transcription.
JOURNAL OF VIROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yuexuan Long, Zhenping Liu, Pengcheng Wang, Hang Yang, Yuejin Wang, Sainan Zhang, Xianlong Zhang, Maojun Wang
Summary: Structural variations (SVs) play a significant role in transcriptional regulation, with some SVs affecting TAD boundary regions and disrupting TAD organization; SVs tend to occur in TAD interior, possibly due to relaxed evolutionary selection pressure; Tetraploid cottons show biased evolution in SV-mediated disruption of 3D genome structure relative to diploids.
Article
Biochemical Research Methods
Jhen Yuan Yang, Jia-Ming Chang
Summary: Recent evidence shows that the three-dimensional chromosome structure is important for genomic function. This study proposes a novel approach using convolutional and residual neural networks to recognize topologically associating domains (TADs) as image patterns. The results demonstrate high performance across species and cell types, indicating the practicality of the TAD recognition model.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Jacob T. Sanders, Rosela Golloshi, Priyojit Das, Yang Xu, Peyton H. Terry, Darrian G. Nash, Job Dekker, Rachel Patton McCord
Summary: This study investigates the effects of chromatin extension during volume changes using low-salt swelling and genome-wide chromosome conformation capture technology. The results show that global genome structure remains stable despite significant nuclear volume swelling. Extension of the local chromatin fiber leads to changes in contact probabilities, but loops, TADs, active and inactive compartments, and chromosome territories are maintained. This suggests that genome topology is robust to chromatin fiber extension and shape changes.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Xiaoqing Peng, Yiming Li, Mengxi Zou, Xiangyan Kong, Yu Sheng
Summary: In this study, a method named CATAD is proposed to identify topologically associating domains (TADs) based on the core-attachment structure model. The CATAD method identifies the core of TADs based on local density and cosine similarity and determines the surrounding attachments based on boundary insulation. The results show that CATAD outperforms other methods in identifying TAD boundaries and is robust to different resolutions of Hi-C matrices.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Immunology
Wenliang Wang, Aditi Chandra, Naomi Goldman, Sora Yoon, Emily K. Ferrari, Son. C. Nguyen, Eric F. Joyce, Golnaz Vahedi
Summary: The study shows that TCF-1 plays a role in controlling the global genome organization during T cell development. It alters the structure of topologically associating domains and promotes interactions between previously insulated regulatory elements and target genes.
Article
Biochemistry & Molecular Biology
Yi Liao, Xinwen Zhang, Mahul Chakraborty, J. J. Emerson
Summary: Research on the molecular evolution of TADs in Drosophila species reveals that a significant proportion of their genomes retain conserved TADs. Comparative genomic analysis shows that chromosomal rearrangement breakpoints are enriched at TAD boundaries, while genes within conserved TADs exhibit lower expression divergence. Structural variants (SVs) identified from different Drosophila strains demonstrate evidence of selection acting on SVs at TAD boundaries, with different types of selection for deletions and tandem duplications.
Article
Genetics & Heredity
Chenguang Zhao, Tong Liu, Zheng Wang
Summary: This study investigates the functional similarities of protein-coding genes within topologically associating domains (TADs) and gap regions. It is found that genes within the same TAD or gap region are more likely to share similar protein functions. A network model based on Hi-C contacts and TAD relationships shows better performance in predicting gene functions.
Review
Cell Biology
Juan J. Tena, Jose M. Santos-Pereira
Summary: TADs in animal genomes serve as structural scaffolds for gene regulation, influencing the establishment of regulatory landscapes. Recent advancements have shed light on the roles of TADs in gene regulation and development, with restructuring TADs potentially leading to pathological conditions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Sarah E. Gilbertson, Hannah C. Walter, Katherine Gardner, Spencer N. Wren, Golnaz Vahedi, Amy S. Weinmann
Summary: Distinguishing between conserved and divergent regulatory mechanisms is crucial for translating preclinical research from mice to humans. Evolutionary genome rearrangements disrupt TAD boundaries, enabling sequence-conserved enhancer elements from divergent genomic locations between species to create unique regulatory modules.
Article
Biochemistry & Molecular Biology
Guifang Du, Hao Li, Yang Ding, Shuai Jiang, Hao Hong, Jingbo Gan, Longteng Wang, Yuanping Yang, Yinyin Li, Xin Huang, Yu Sun, Huan Tao, Yaru Li, Xiang Xu, Yang Zheng, Junting Wang, Xuemei Bai, Kang Xu, Yaoshen Li, Qi Jiang, Cheng Li, Hebing Chen, Xiaochen Bo
Summary: Recent studies have shown the association between the 3D structure of chromatin and cancer progression. This study investigates the hierarchical TAD structures in cancers and their dynamic changes in relation to transcriptional abnormalities, revealing the significant impact on cancer prognosis. The results emphasize the importance of hierarchical chromatin organization in cancer development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Genetics & Heredity
Christophe Tav, Eric Fournier, Michele Fournier, Fatemeh Khadangi, Audrey Baguette, Maxime C. Cote, Maruhen A. D. Silveira, Felix-Antoine Berube-Simard, Guillaume Bourque, Arnaud Droit, Steve Bilodeau
Summary: Transcription-factor binding and reorganization of coregulators can regulate gene expression. Hormone-induced gene response can be mediated by changes in the distribution of coregulators in chromatin regions. These results support a model where signal-induced transcription factors induce regional effects, redefining the concept of direct and indirect effects on target genes.
FRONTIERS IN GENETICS
(2023)
Review
Genetics & Heredity
Samuel Jianjie Yeo, Chen Ying, Melissa Jane Fullwood, Vinay Tergaonkar
Summary: This review discusses the roles of noncoding RNAs (ncRNAs) in regulating the form and function of topologically associating domains (TADs), including moderating loop extrusion through interactions with architectural proteins and facilitating TAD phase separation. The article also proposes future studies and directions to investigate these phenomena.
TRENDS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
