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Biochemical Research Methods
Joachim Wolff, Rolf Backofen, Bjoern Gruening
Summary: The single-cell Hi-C clustering approach proposed in this study utilizes an approximate nearest neighbors method based on locality-sensitive hashing to reduce computational resources. It shows advantages in processing large-scale data compared to competitive methods.
Article
Multidisciplinary Sciences
Luming Meng, Chenxi Wang, Yi Shi, Qiong Luo
Summary: There is a strong demand for methods that can efficiently reconstruct valid super-resolution intact genome 3D structures from sparse and noise single-cell Hi-C data. The authors developed the Single-Cell Chromosome Conformation Calculator (Si-C) within the Bayesian theory framework for this purpose, demonstrating its potential for visualizing and investigating interactions between all chromatin loci at the genome scale in individual cells. This method is essential in investigating chromosome folding and can reveal cell-to-cell varying domain structures and hyperfine structures in domains, such as loops.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Catherine E. Scull, Guy Twa, Yinfeng Zhang, Naiheng J. Yang, Robert N. Hunter III, Corinne E. Augelli-szafran, David A. Schneider
Summary: A newly identified ribosome biogenesis inhibitor, RBI2, has been shown to inhibit multiple types of cancer cells by inducing rapid polyadenylation and degradation of ribosomal RNA. This mechanism of action is distinct from previously described compounds and offers a potential novel pathway for cancer therapeutics targeting ribosome synthesis. This study reveals the importance of ribosome biogenesis in cancer cell growth and highlights the potential of RBI2 as a promising cancer therapeutic.
Article
Multidisciplinary Sciences
Ke Xiao, Dan Xiong, Gong Chen, Jinsong Yu, Yue Li, Kening Chen, Lu Zhang, Yangyang Xu, Qian Xu, Xi Huang, Anran Gao, Kai Cao, Keji Yan, Jinxia Dai, Xueying Hu, Yijun Ruan, Zhenfang Fu, Guoliang Li, Gang Cao
Summary: This study demonstrates a genome-wide trans-species chromatin interaction between pseudorabies virus (PRV) and host cells, where the viral genome is delivered into the open and active chromatin zone by the host DNA binding protein RUNX1. This facilitates viral gene transcription by hijacking host transcription machinery, a process significantly inhibited by either a RUNX1 inhibitor or RNA interference. These findings provide insights into herpesvirus genome transcription and suggest new research directions in this area.
Article
Multidisciplinary Sciences
Martin Franke, Elisa De la Calle-Mustienes, Ana Neto, Maria Almuedo-Castillo, Lbai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Jose M. Santos-Pereira, Jose L. Gomez-Skarmeta
Summary: CTCF plays a critical role in animal development by regulating three-dimensional chromatin structure and enhancer-promoter interactions, essential for controlling the expression of thousands of genes. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), impacting gene regulation during development. Loss of CTCF leads to disrupted chromatin structure and affects the expression of developmental regulators, highlighting its essential role in providing structural context for enhancer-promoter interactions.
NATURE COMMUNICATIONS
(2021)
Review
Genetics & Heredity
Britta A. M. Bouwman, Nicola Crosetto, Magda Bienko
Summary: The advent of high-throughput chromosome conformation capture (Hi-C) over a decade ago has revolutionized the field of 3D genomics. It has enabled mapping of the 3D genome and provided insights into the packaging of DNA in the nucleus and the orchestration of vital functions. Recent advances in spatial genomics technologies have further revealed variations in genome sequence and 3D genome organization within cells in their tissue context.
TRENDS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yi Xiang See, Kaijing Chen, Melissa J. Fullwood
Summary: The MYC oncogene is frequently dysregulated in various cancer cell types, making it an attractive target for cancer therapy. This study found that MYC overexpression leads to MYC binding at super-enhancers and alters the chromatin landscape of the cancer genome. These findings have implications for understanding and targeting MYC-driven cancers.
Article
Oncology
Ruth Q. Jacobs, Kaila B. Fuller, Stephanie L. Cooper, Zachariah Carter, Marikki Laiho, Aaron L. Lucius, David A. Schneider
Summary: This study evaluates the specificity of the compound BMH-21 on transcription by Pols I, II, and III. The results show that Pol I is more sensitive to inhibition by BMH-21 compared to Pols II and III. These findings support the ongoing development of BMH-21 and its derivatives as potential therapeutic agents.
Article
Multidisciplinary Sciences
Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Melanie Miranda, Vincent Piras, Jeril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sebastien Bloyer, Amelie Leforestier, Eric F. Joyce, David Holcman, Daan Noordermeer
Summary: Topologically Associating Domains (TADs) separate vertebrate genomes into isolated regulatory neighborhoods, and the clustering of CTCF binding sites contributes to blocking loop extrusion and insulation between TADs.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Christian-Alexander Dudek, Dieter Jahn
Summary: PRODORIC is one of the largest collections of prokaryotic transcription factor binding sites worldwide, with the latest version featuring a fully API-based database backend, updated visualization tools, reannotation of the dataset for improved quality, and the addition of new transcription factors and organisms. The database is publicly available at https://www.prodoric.de.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Kevin M. Andre, Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, Julie Soutourina
Summary: Chromatin organization is crucial for transcriptional regulation. Mediator and RSC contribute to chromatin remodeling and transcriptional regulation by establishing physical contact and coordinating their functions.
Review
Biochemistry & Molecular Biology
Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Ahmed Al-Harrasi
Summary: The genome is the most functional part of a cell and is organized in a compact three-dimensional structure. Despite TADs being major contributors to 3D genome organization, they are absent in Arabidopsis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Dean Huang, Anna E. Johnson, Brandon S. Sim, Teresa W. Lo, Houra Merrikh, Paul A. Wiggins
Summary: Quantitative characterization of nucleic-acid-bound molecular motors' dynamics in living cells is crucial for understanding the mechanistic basis of the central dogma. Lag-time analysis was developed to measure in vivo dynamics, providing quantitative locus-specific measurements of fork velocity and replisome pause durations. The observed dynamics are both locus and time dependent, even in wild-type cells, showing locus-specific pauses and temporal fork velocity oscillations.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Oleg Bylino, Airat N. Ibragimov, Anna E. Pravednikova, Yulii Shidlovskii
Summary: Chromosome conformation capture methods (C-methods) are important tools for analyzing the spatial interactions between DNA regions. Understanding the basic steps of the chromatin conformation capture procedure (3C) is crucial, and optimizing conditions for cell treatment can lead to more efficient experiments.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Jia-Yong Zhong, Longjian Niu, Zhuo-Bin Lin, Xin Bai, Ying Chen, Feng Luo, Chunhui Hou, Chuan-Le Xiao
Summary: By using the high-throughput Pore-C technique, researchers have discovered extensive and regionally restricted clusters of single-allele topologies in two human cell types, which aggregate into canonical 3D genome structures. They also observed a significant portion of multi-contact reads spanning multiple compartments of the same chromatin type over long distances. Moreover, the single-allele topology clusters are cell type-specific. These findings provide global characterization of single-allele topologies and reveal the principles of genome folding.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Jackson Buss, Carla Coltharp, Gleb Shtengel, Xinxing Yang, Harald Hess, Jie Xiao
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Biochemistry & Molecular Biology
Carla Coltharp, Jie Xiao
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Biochemistry & Molecular Biology
Zhixin Lyu, Carla Coltharp, Xinxing Yang, Jie Xiao
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Chemistry, Physical
Yinchan Luo, Xinxing Yang, Xiaofang Tan, Ligeng Xu, Zhuang Liu, Jie Xiao, Rui Peng
Review
Microbiology
Jie Xiao, Erin D. Goley
CURRENT OPINION IN MICROBIOLOGY
(2016)
Article
Multidisciplinary Sciences
Carla Coltharp, Jackson Buss, Trevor M. Plumer, Jie Xiao
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Review
Microbiology
Jie Xiao, Yves F. Dufrene
NATURE MICROBIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Jackson A. Buss, Nick T. Peters, Jie Xiao, Thomas G. Bernhardt
MOLECULAR MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Selamawit Abi Woldemeskel, Ryan McQuillen, Alex M. Hessel, Jie Xiao, Erin D. Goley
MOLECULAR MICROBIOLOGY
(2017)
Article
Biochemical Research Methods
Gary C. H. Mo, Brian Ross, Fabian Hertel, Premashis Manna, Xinxing Yang, Eric Greenwald, Chris Booth, Ashlee M. Plummer, Brian Tenner, Zan Chen, Yuxiao Wang, Eileen J. Kennedy, Philip A. Cole, Karen G. Fleming, Amy Palmer, Ralph Jimenez, Jie Xiao, Peter Dedecker, Jin Zhang
Editorial Material
Multidisciplinary Sciences
Jie Xiao, Taekjip Ha
Article
Multidisciplinary Sciences
Xinxing Yang, Zhixin Lyu, Amanda Miguel, Ryan McQuillen, Kerwyn Casey Huang, Jie Xiao
Article
Multidisciplinary Sciences
Xiaoli Weng, Christopher H. Bohrer, Kelsey Bettridge, Arvin Cesar Lagda, Cedric Cagliero, Ding Jun Jin, Jie Xiao
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biophysics
Christopher H. Bohrer, Kelsey Bettridge, Jie Xiao
BIOPHYSICAL JOURNAL
(2017)