Article
Biochemistry & Molecular Biology
Maojun Wang, Jianying Li, Pengcheng Wang, Fang Liu, Zhenping Liu, Guannan Zhao, Zhongping Xu, Liuling Pei, Corrinne E. Grover, Jonathan F. Wendel, Kunbo Wang, Xianlong Zhang
Summary: Transposable element (TE) amplification plays a crucial role in mediating genome size expansion and evolution, with lineage-specific TE amplification contributing to large genome size differences in cotton species. The study also reveals changes in chromatin status in gene regions due to TE amplification and highlights the recent amplification of TEs affecting the formation of lineage-specific TAD boundaries in plants.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Benjamin Lebeau, Maika Jangal, Tiejun Zhao, Cheng Kit Wong, Nolan Wong, Eduardo Cepeda Canedoa, Steven Hebert, Adriana Aguilar-Mahecha, Catherine Chabot, Marguerite Buchanan, Rachel Catterall, Luke McCaffrey, Genevieve Debloise, Claudia Kleinman, Morag Park, Mark Basik, Michael Witcher
Summary: The relationship between deregulated chromatin structure and cancer progression is still unclear. Loss of CTCF in breast cancer leads to changes in chromatin structure and epigenetic programming, increasing cell invasion. However, this change in chromatin structure also increases susceptibility to mTOR inhibitors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Xuelong Wang, Jizhou Yan, Zhao Ye, Zhiqiang Zhang, Sheng Wang, Shuang Hao, Baiyong Shen, Gang Wei
Summary: This study revealed the close connection between 3D genome reorganization, chromatin accessibility, and gene transcription in doxorubicin-resistant breast cancer, providing new insights into the epigenomic mechanisms of doxorubicin resistance.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Jiaman Zhang, Pengliang Liu, Mengnan He, Yujie Wang, Hua Kui, Long Jin, Diyan Li, Mingzhou Li
Summary: This study investigated the 3D genome organization and transcriptome characterization of adipose depots in two different pig breeds. While large-scale compartments and TADs were conserved between Bama pigs and wild boar, fine-scale PEIs were extensively reorganized. The chromatin architecture of these two pig breeds was reorganized in a depot-specific manner. These findings contribute to our understanding of the regulatory mechanism underlying phenotypic differences between Bama pigs and wild boar.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Daria Kostiniuk, Hely Tamminen, Pashupati P. Mishra, Saara Marttila, Emma Raitoharju
Summary: The nc886 locus is not polymorphically imprinted in non-human primates and guinea pigs, unlike in humans, suggesting that animal models are not applicable for nc886 research. The data obtained suggests that the nc886 region may be classically imprinted in great apes and potentially also in Old World monkeys.
Review
Cell Biology
Sergey Ulianov, Sergey Razin
Summary: Advancements in biochemistry and microscopy technology have enabled comprehensive studies of 3D genome organization in individual cells, revealing the internal structures of genome folding and cell-cycle dynamics. 3D modeling allows for the investigation of the physical mechanisms underlying genome folding.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Angsheng Li, Guangjie Zeng, Haoyu Wang, Xiao Li, Zhihua Zhang
Summary: This study reports a new generation TLD detection algorithm called deDoc2, which decodes the hierarchy of TLDs in single cells. By using dynamic programming, deDoc2 identifies genome partitions with minimal structure entropy for both whole and local contact matrix. The results show that the hierarchy of TLDs in single cells is highly dynamic during cell cycle and among human brain cortex cells, and it is associated with cellular identity and functions.
Article
Biology
Sofiene Seef, Julien Herrou, Paul de Boissier, Laetitia My, Gael Brasseur, Donovan Robert, Rikesh Jain, Romain Mercier, Eric Cascales, Bianca H. Habermann, Tam Mignot
Summary: Myxococcus xanthus, a soil bacterium, preys collectively on prey colonies using A-motility and contact-dependent killing as central predatory mechanisms. The newly discovered Kil-like systems form a new class of Tad-like machineries in predatory bacteria, with a conserved function in predator-prey interactions. This study also reveals a novel cell-cell interaction function for bacterial pili-like assemblages.
Article
Biochemical Research Methods
Spiro C. Stilianoudakis, Maggie A. Marshall, Mikhail G. Dozmorov
Summary: The preciseTAD framework, trained on high-resolution genome annotation data, accurately predicts 3D domain boundaries at base-pair resolution, providing a new tool for better understanding how genomic regulators shape the 3D structure of the genome.
Article
Biotechnology & Applied Microbiology
Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Summary: The newly developed algorithm deTOKI successfully identifies TAD-like domains in single cells, indicating that these structures are prevalent and tightly regulated in single cells.
Article
Multidisciplinary Sciences
Guang Shi, D. Thirumalai
Summary: The authors developed a computational method based on the maximum entropy principle to construct a structural ensemble of genomes using imaging data. This work revealed three-way contacts between loci and extensive conformational heterogeneity. Single-cell imaging techniques were used to determine the 3D coordinates of genomic loci, and the computational method (DIMES) was introduced to generate a unique ensemble of 3D chromatin structures. The DIMES method can quantify heterogeneity in the shapes of chromatin structures.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Kyukwang Kim, Insu Jang, Mooyoung Kim, Jinhyuk Choi, Min-Seo Kim, Byungwook Lee, Inkyung Jung
Summary: The paragraph discusses the tight relationship between three-dimensional genome organization and gene regulation, particularly in cancer where genomic rearrangements can disrupt the 3D genome. Challenges remain in understanding the pathogenicity of the 3D cancer genome, but the updated 3DIV tool provides a comprehensive resource to explore the gene regulatory effects of both normal and cancer 3D genome.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Tharvesh M. Liyakat Ali, Annael Brunet, Philippe Collas, Jonas Paulsen
Summary: The study reveals that long-range interactions of TADs are associated with key features of chromatin organization, and domains forming large TAD cliques tend to be repressive.
Article
Multidisciplinary Sciences
Yanwu Guo, Cristina Tocchini, Rafal Ciosk
Summary: This study identified a conserved gene clk-2 as a key player in nematode NMD pathway, while its human counterpart TELO2 is also implicated in NMD. Variants in TELO2 have been linked to an intellectual disability disorder, suggesting a potential role in the NMD pathway.
Article
Ecology
Christina L. Wiesmann, Yue Zhang, Morgan Alford, Corri D. Hamilton, Manisha Dosanjh, David Thoms, Melanie Dostert, Andrew Wilson, Daniel Pletzer, Robert E. W. Hancock, Cara H. Haney
Summary: Members of the bacterial genus Pseudomonas can form mutualistic, commensal, and pathogenic associations with diverse hosts. The study found that the regulatory gene ColR/S is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens, but there are differences in the regulon. ColR/S allows Pseudomonas to sense and respond to a host, and the divergence of the ColR regulon may be related to different lifestyles.
Article
Genetics & Heredity
Ittai E. Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E. Blake, Yoav Gilad
Article
Biochemistry & Molecular Biology
Lauren E. Blake, Julien Roux, Irene Hernando-Herraez, Nicholas E. Banovich, Raquel Garcia Perez, Chiaowen Joyce Hsiao, Ittai Eres, Claudia Cuevas, Tomas Marques-Bonet, Yoav Gilad