Article
Biochemistry & Molecular Biology
Marina Feric, Tyler G. Demarest, Jane Tian, Deborah L. Croteau, Vilhelm A. Bohr, Tom Misteli
Summary: Mitochondria contain an autonomous genome organized into nucleoids, and the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid) is phase separation. The major mtDNA-binding protein TFAM can spontaneously phase separate into droplets with slow internal dynamics in vitro, which recapitulates the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to cellular stress, as seen in patients with Hutchinson-Gilford Progeria Syndrome (HGPS), pointing to phase separation as an evolutionarily conserved mechanism of genome organization.
Review
Oncology
Emanuele Vitale, Mila Gugnoni, Alessia Ciarrocchi
Summary: Enhancers are cis-acting regulatory elements that can promote gene expression in a distance- and orientation-independent manner. They work in a dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The interactions among enhancers vary in their nature and extent, contributing to the regulation of complex biological processes like cancer development.
Article
Biology
Tetsuya Yamamoto, Takahiro Asanuma, Yota Murakami
Summary: In this study, a kinetic model was used to evaluate the relationship between heterochromatin assembly, small RNA production, and histone methylation in fission yeast. The theory of heterochromatin assembly was proposed by considering the connectivity of tandemly repeated genes along the chromatin in the kinetic equations of small RNA production and histone methylation. The theory predicts the steady production of small RNAs due to the polymeric nature of tandemly repeated genes and the compaction of these genes suppresses the production of small RNAs, which is consistent with recent experiments. This theory can be applied to small RNA-dependent gene silencing in higher organisms.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Robin Weinmann, Lukas Frank, Karsten Rippe
Summary: This article discusses recent advancements in studying the local properties and compositional dynamics of chromatin, as well as their functional implications in protein and RNA enrichment and genome accessibility.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Rei Mitamura, Masataka Nakano, Motoki Isono, Kiamu Kurosawa, Tatsuki Fukami, Miki Nakajima
Summary: This study revealed that PXR interacts with paraspeckle components NEAT1_2 and DAZAP1 to suppress CYP3A4 induction by PXR, and the interaction is dissociated by PXR ligands. This finding provides a novel concept that paraspeckles formed by liquid-liquid phase separation potentially affect drug metabolism via negative regulation of PXR function.
DRUG METABOLISM AND DISPOSITION
(2023)
Article
Cell Biology
Kyoung-Jae Choi, My Diem Quan, Chuangye Qi, Joo-Hyung Lee, Phoebe S. Tsoi, Mahla Zahabiyon, Aleksandar Bajic, Liya Hu, B. V. Venkataram Prasad, Shih-Chu Jeff Liao, Wenbo Li, Allan Chris M. Ferreon, Josephine C. Ferreon
Summary: Choi et al. found that human NANOG proteins can form gel-like condensates at low concentrations, which play a crucial role in maintaining pluripotency. The unique features of NANOG, including its largely disordered structure and prion-like domain, contribute to its dose-sensitive function as a master transcription factor. NANOG oligomerization is essential for bridging DNA elements and specific chromatin interactions.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Liyang Wu, Ting Pan, Mo Zhou, Tao Chen, Shiyu Wu, Xi Lv, Jun Liu, Fei Yu, Yuanjun Guan, Bingfeng Liu, Wanying Zhang, Xiaohui Deng, Qianyu Chen, Anqi Liang, Yingtong Lin, Lilin Wang, Xiaoping Tang, Weiping Cai, Linghua Li, Xin He, Hui Zhang, Xiancai Ma
Summary: CBX4 has been identified as a key factor in HIV-1 latency, acting as a bridge between the repressor complexes PRC1 and PRC2 to maintain viral latency. This discovery sheds light on potential interventions for reactivating latent HIV-1 infection.
Article
Biochemistry & Molecular Biology
Liguo Zhang, Yang Zhang, Yu Chen, Omid Gholamalamdari, Yuchuan Wang, Jian Ma, Andrew S. Belmont
Summary: The study shows that gene distance to nuclear speckles is a better predictor of gene expression levels than radial positioning. While only a small portion of the genome exhibits significant shifts in relative nuclear speckle distances between human cell lines, these changes are closely linked to cell type-specific gene expression.
Editorial Material
Biochemistry & Molecular Biology
Paul D. Kaufman, Sui Huang, Thoru Pederson
Summary: This conference explored the investigation of nuclear bodies, revealing new findings that confirmed and expanded the understanding of genome activity.
Article
Chemistry, Multidisciplinary
Ruo-Chen Guo, Xue-Hao Zhang, Peng-Sheng Fan, Ben-Li Song, Zhi-Xiang Li, Zhong-Yu Duan, Zeng-Ying Qiao, Hao Wang
Summary: A novel in vivo self-assembly strategy is developed to induce phase separation of cell membrane, improving the internalization of therapeutic peptides and enhancing drug delivery efficacy, particularly in cancer therapy.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Adam J. Stevens, Andrew R. Harris, Josiah Gerdts, Ki H. Kim, Coralie Trentesaux, Jonathan T. Ramirez, Wesley L. McKeithan, Faranak Fattahi, Ophir D. Klein, Daniel A. Fletcher, Wendell A. Lim
Summary: Cell adhesion molecules play a crucial role in various cellular processes, and their synthetic counterparts can be generated by combining extracellular interactions with intracellular domains. These synthetic molecules allow for customized cell-cell interactions with properties similar to native interactions. The intracellular domains determine the interface morphology and mechanics, while the extracellular interaction domains specify the connectivity between cells. This toolkit of synthetic cell adhesion molecules enables the assembly of multicellular architectures and the systematic remodeling of native tissues, providing insights into the evolution of different classes of cell-cell interfaces. Overall, these tools have significant implications for cell and tissue engineering and the study of multicellular organization.
Article
Biotechnology & Applied Microbiology
Zachary Gorman, Jianchi Chen, Adalberto A. Perez de Leon, Christopher Michael Wallis
Summary: This study analyzed the mitochondrial genome of a Trichoderma strain and compared four different assembly methods. The hybrid assembler, MaSuRCA, was found to be the most effective. By comparing the genes of the PAR3 strain, unique genes were identified, which could have important implications for the applications of Trichoderma.
Article
Multidisciplinary Sciences
Qin Peng, Ziliang Huang, Kun Sun, Yahan Liu, Chi Woo Yoon, Reed E. S. Harrison, Danielle L. Schmitt, Linshan Zhu, Yiqian Wu, Ipek Tasan, Huimin Zhao, Jin Zhang, Sheng Zhong, Shu Chien, Yingxiao Wang
Summary: Genome architecture and organization are crucial for cell life, but how they coordinate gene expression and determine cell fate at the single cell level remains unknown. The researchers developed a system called SIMBA which allows for simultaneous imaging and manipulation of genomic loci using biomolecular assemblies. This system can enhance imaging signals and recruit epigenetic modulators to repress transcription at specific genomic loci, making it a valuable tool for visualizing and manipulating gene expression in living cells.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Rui Wang, Qiqin Xu, Chenlu Wang, Kai Tian, Hui Wang, Xiong Ji
Summary: Proteomic profiling identified ZBTB21 as a transcription factor that contributes to the chromatin binding and transcriptional repression of cohesin in 3D chromatin structures. Other ZBTB factors also interact with cohesin, and double degradation of ZBTB21 and ZBTB7B leads to a further decrease in cohesin chromatin occupancy.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Binbin Lu, Meng Liu, Liang Gu, Ying Li, Shijun Shen, Gangqiang Guo, Fei Wang, Xiaohui He, Yuemeng Zhao, Xiaomin Shang, Liping Wang, Guang Yang, Qianshu Zhu, Jun Cao, Cizhong Jiang, Richard Culleton, Gang Wei, Qingfeng Zhang
Summary: The study identifies HMGB1 as a critical architectural factor in the high-order genome organization and gene expression regulation in the malaria parasite Plasmodium falciparum. Loss of HMGB1 disrupts chromosome organization and leads to dysregulated gene expression, particularly silencing of the primary virulence genes. The reconstitution of nuclear organization by complementation of HMGB1 rescues the exclusive expression of the virulence gene family, indicating HMGB1 as a potential target for antimalarial strategies.
Article
Biotechnology & Applied Microbiology
Vuthy Ea, Tom Sexton, Thierry Gostan, Laurie Herviou, Marie-Odile Baudement, Yunzhe Zhang, Soizik Berlivet, Marie-Noelle Le Lay-Taha, Guy Cathala, Annick Lesne, Jean-Marc Victor, Yuhong Fan, Giacomo Cavalli, Thierry Fome
Article
Biochemistry & Molecular Biology
Ghislain Auclair, Julie Borgel, Lionel A. Sanz, Judith Vallet, Sylvain Guibert, Michael Dumas, Patricia Cavelier, Michael Girardot, Thierry Forne, Robert Feil, Michael Weber
Article
Biochemistry & Molecular Biology
Marie-Odile Baudement, Axel Cournac, Franck Court, Marie Seveno, Hugues Parrinello, Christelle Reynes, Robert Sabatier, Tristan Bouschet, Zhou Yi, Sephora Sallis, Mathilde Tancelin, Cosette Rebouissou, Guy Cathala, Annick Lesne, Julien Mozziconacci, Laurent Journot, Thierry Forne
Article
Genetics & Heredity
Jonas Paulsen, Tharvesh M. Liyakat Ali, Maxim Nekrasov, Erwan Delbarre, Marie-Odile Baudement, Sebastian Kurscheid, David Tremethick, Philippe Collas
Article
Oncology
Amaelle Otandault, Jean-Daniel Abraham, Zahra Al Amir Dache, Abdelnaby Khalyfa, Isabelle Jariel-Encontre, Thierry Forne, Corinne Prevostel, Salem Chouaib, David Gozal, Alain R. Thierry
BRITISH JOURNAL OF CANCER
(2020)
Article
Biochemistry & Molecular Biology
Kathryn Vaillancourt, Jennie Yang, Gary G. Chen, Volodymyr Yerko, Jean-Francois Theroux, Zahia Aouabed, Alberto Lopez, Kimberly C. Thibeault, Erin S. Calipari, Benoit Labonte, Naguib Mechawar, Carl Ernst, Corina Nagy, Thierry Forne, Eric J. Nestler, Deborah C. Mash, Gustavo Turecki
Summary: The study explored the role of DNA methylation in cocaine dependence and found a correlation between hypomethylation of the IRX2 gene and addiction. The findings suggest that cocaine-related hypomethylation of IRX2 contributes to the development and maintenance of cocaine dependence through alterations in 3D chromatin structure.
MOLECULAR PSYCHIATRY
(2021)
Article
Cell Biology
Sebastien Calvet, Sephora Sallis, Nehme Saksouk, Cosette Rebouissou, Catherine Teyssier, Annick Lesne, Florence Cammas, Thierry Forne
Summary: About half of the mammalian genome is made up of repeated elements, and endogenous retroviruses (ERVs) are known to affect gene expression and cancer development. The HP1 protein has a crucial role in establishing and functioning heterochromatin, and its loss in hepatocytes results in the reactivation of specific ERVs and the development of liver tumors. This study discovered that certain HP1-dependent ERVs located upstream of genes Mbd1 and Trim24 can act as alternative promoters or potential enhancers, forming a loop with promoters of endogenous genes depending on the genomic context and HP1 expression level.
Article
Biotechnology & Applied Microbiology
Julia Madsen-Osterbye, Mohamed Abdelhalim, Marie-Odile Baudement, Philippe Collas
Summary: LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes, and their repositioning partially correlates with gene expression changes during adipogenesis.
Article
Genetics & Heredity
Kim Philipp Jablonski, Leopold Carron, Julien Mozziconacci, Thierry Forne, Marc-Thorsten Huett, Annick Lesne
Summary: In this study, the researchers investigated the distribution of disease-associated single-nucleotide polymorphisms (SNPs) in relation to topologically associating domains (TADs) and their borders. They found that a fraction of diseases, especially cancers, showed a preferential localization of risk loci in these genomic regions. The results suggest that genetic variations affecting the genome partitioning within TADs may contribute to the genetic risk of certain diseases, particularly cancers.
Proceedings Paper
Oncology
K. P. Jablonski, C. Fretter, L. Carron, T. Forne, M. -T. Hutt, A. Lesne
PHYSICS OF CANCER: INTERDISCIPLINARY PROBLEMS AND CLINICAL APPLICATIONS (PC IPCA)
(2017)
Proceedings Paper
Oncology
Oleg B. Naimark, Aleksandr S. Nikitiuk, Marie-Odile Baudement, Thierry Forne, Annick Lesne
PHYSICS OF CANCER: INTERDISCIPLINARY PROBLEMS AND CLINICAL APPLICATIONS (PC'16)
(2016)