Article
Biochemistry & Molecular Biology
Jonna Heldrich, Carolyn R. Milano, Tovah E. Markowitz, Sarah N. Ur, Luis A. Vale-Silva, Kevin D. Corbett, Andreas Hochwagen
Summary: Successful meiotic recombination requires conserved axis proteins, which distribute on chromosomes through two independent pathways: a cohesin-dependent pathway and a cohesin-independent pathway. These pathways result in a stereotypic distribution pattern and the formation of chromatin islands that influence chromosome structure.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yu Wei Zhang, Lingxi Chen, Shuai Cheng Li
Summary: Topologically associated domains (TADs) are crucial structural units in chromatin. RNA-associated interactions (RAIs) have been found to be associated with TAD-like domains (TLDs). A domain detection algorithm called SuperTLD was proposed to decode hierarchical TLDs from RAIs. Comparison between TLDs and TADs identified from Hi-C datasets showed moderate similarity in hierarchies and higher similarity in finer structures. Enrichment analysis revealed the novelty of TLDs in terms of boundaries and epigenetic characteristics, suggesting a close relationship between TLDs and gene regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Rakesh Das, Takahiro Sakaue, G. Shivashankar, Jacques Prost, Tetsuya Hiraiwa, Naama Barkai
Summary: This study constructs a polymer physics model based on the mechanistic scheme of Topoisomerase-II to investigate its effect on the spatial organization of interphase chromatin. The simulations show that Topoisomerase-II can phase separate chromatin into eu- and heterochromatic regions, with a wall-like organization of the euchromatic regions. The ability of the euchromatic regions to cross each other, induced by the enzymatic activity of Topoisomerase-II, leads to this phase separation. The model is extended to a bidisperse setting, and the characteristic features of enzymatic activity-driven phase separation are observed. These findings highlight the critical role of enzymatic activity in chromatin organization.
Review
Genetics & Heredity
Ian R. Henderson, Kirsten Bomblies
Summary: Recombination is nearly ubiquitous and important in eukaryotes for chromosome segregation during gamete production, with variation in rates among and within species. While generally beneficial, recombination may also have costs and its variation remains unclear. Environmental sensitivity of meiosis and recombination rates may relate to adaptation and have implications for understanding recombination rate evolution.
ANNUAL REVIEW OF GENETICS, VOL 55
(2021)
Article
Genetics & Heredity
Rahia Mashoodh, Lisa C. Hulsmann, Frances L. Dearden, Nozomi Takahashi, Carol Edwards, Anne C. Ferguson-Smith
Summary: In this study, imprinting genes were used as a model system to investigate the relationship between the parental origin of chromosomes, the localization of genes within the cell nucleus, and their active expression. The results indicate that there is a small preference for the paternal chromosome to be closer to the periphery, but there is a significant correlation between transcription and distance to the edge of the nucleus for the Gtl2/Meg3 gene. Furthermore, a chromosome nearer the periphery is just as likely to express the gene as the chromosome further away. These findings suggest that the parental origin of the chromosome may not be as important as the transcription of the gene in defining the position of the imprinted region within the nucleus.
Article
Biotechnology & Applied Microbiology
Megan Justice, Audra F. Bryan, Juanita C. Limas, Jeanette Gowen Cook, Jill M. Dowen
Summary: The study found that loss of WIZ leads to changes in cohesin localization on chromatin, distinct from loss of G9a and canonical cohesin unloading factor WAPL. Ectopic cohesin binding sites were observed after the loss of WIZ, enriched for activating histone modifications and transcription factor motifs. WIZ appears to function independently of its previously identified role in heterochromatin formation.
Article
Biochemistry & Molecular Biology
Kei Yamaya, Bin Wang, Nadin Memar, Arome Solomon Odiba, Alexander Woglar, Anton Gartner, Anne M. Villeneuve
Summary: RAD54 family DNA translocases, together with RAD51 recombinases, play a role in maintaining genome stability. Studying the functions of RAD54 paralogs RAD-54.L and RAD-54.B in Caenorhabditis elegans during meiotic prophase reveals their distinct contributions to the dynamics of RAD-51 association with DNA and meiotic double-strand break repair. RAD-54.L is essential for RAD-51 removal from meiotic double-strand break sites, while RAD-54.B prevents excessive accumulation of RAD-51 on unbroken DNA. This study provides insights into the division of labor among RAD-54 paralogs in promoting efficient homologous recombination and preventing deleterious effects of unproductive RAD-51 association.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan M. J. Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan H. Gibcus, Job Dekker
Summary: Chromosome conformation capture assays, such as Hi-C and Micro-C, are used to map chromatin interactions and understand chromosome folding mechanisms. Through systematic evaluation of experimental parameters, an optimized Hi-C protocol was developed for detecting loops and compartments, improving the ability to study chromosome organization.
Review
Oncology
Kosuke Yamaguchi, Xiaoying Chen, Asami Oji, Ichiro Hiratani, Pierre-Antoine Defossez
Summary: Chromatin changes in cancer have significant implications for gene expression, genome stability, and cancer progression, making them important for diagnosis and treatment.
Article
Biochemistry & Molecular Biology
Ou Fang, Lin Wang, Yuxin Zhang, Jixuan Yang, Qin Tao, Fengjun Zhang, Zewei Luo
Summary: Genetic recombination is a vital process in meiosis, contributing to genome stability and genetic variation for natural and artificial selection, and is influenced by various biological and abiotic factors. Genome polyploidization leads to a significant increase in meiotic recombination frequency, accompanied by other biological changes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Maria Cuacos, Christophe Lambing, Miguel Pachon-Penalba, Kim Osman, Susan J. Armstrong, Ian R. Henderson, Eugenio Sanchez-Moran, F. Christopher H. Franklin, Stefan Heckmann
Summary: In Brassica rapa, axis formation and remodelling are crucial for meiotic fidelity, including synapsis and crossover (CO) formation. Mutants of ASY1 and PCH2 show altered distribution of CO, with asy1 plants being sterile and pch2 plants being semi-sterile, making PCH2 a potential target for breeding programs.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Monica M. Franca, Yazmine B. Condezo, Maeva Elzaiat, Natalia Felipe-Medina, Fernando Sanchez-Saez, Sergio Munoz, Raquel Sainz-Urruela, M. Rosario Martin-Hervas, Rodrigo Garcia-Valiente, Manuel A. Sanchez-Martin, Aurora Astudillo, Juan Mendez, Elena Llano, Reiner A. Veitia, Berenice B. Mendonca, Alberto M. Pendas
Summary: A homozygous RAD51B variant was identified in sisters with POI, leading to DNA repair defects and reduced crossovers. This variant also affected RAD51B interactions and replication fork progression, indicating a role in somatic genome stability maintenance.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Microbiology
Aiah Khateb, Sara Gago, Michael Bromley, Malcom Richardson, Paul Bowyer
Summary: Azole resistance in Aspergillus fumigatus is increasing, and non-target-mediated mechanisms contribute to resistance in chronic pulmonary aspergillosis (CPA). This study used whole-genome sequencing to investigate resistance mechanisms. Sixteen azole-resistant A. fumigatus isolates from CPA were sequenced, and genome rearrangements were assessed. Among them, seven CPA isolates showed genomic duplications, including the cyp51A region, which led to increased gene expression. Our findings suggest that aneuploidy is a resistance mechanism in CPA.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Cell Biology
Yaping Huang, Lin Li, Geng An, Xinyan Yang, Manman Cui, Xiuling Song, Jing Lin, Xiaoling Zhang, Zhaokai Yao, Cong Wan, Cai Zhou, Jiexiang Zhao, Ke Song, Shaofang Ren, Xinyu Xia, Xin Fu, Yu Lan, Xuesong Hu, Wen Wang, Mei Wang, Yi Zheng, Kai Miao, Xiaochun Bai, Andrew P. Hutchins, Gang Chang, Shuai Gao, Xiao-Yang Zhao
Summary: Huang, Li, An, Yang, Cui et al. perform a single-cell multi-omics analysis of human spermatogenesis and identify a DNA demethylation event upon meiosis initiation, which is associated with meiotic recombination.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Monika Yadav, Manisha Jalan, Madhulika Srivastava
Summary: The intranuclear position of the TCRb locus is dynamically altered during thymic development and is influenced by the enhancer Eb. The ability to reposition the target locus relative to the chromosome territory highlights a novel aspect of enhancer activity, which may contribute to gene expression regulation. These observations have implications for understanding enhancer function in three-dimensional genome organization.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Honesty Kim, Xiaofan Jin, David S. Glass, Ingmar H. Riedel-Kruse
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2020)
Article
Multidisciplinary Sciences
David S. Glass, Xiaofan Jin, Ingmar H. Riedel-Kruse
Summary: Studying biological networks through delay differential equation models provides important insights, such as parameter reduction, analytical relationships between ODE and DDE models, phase space for autoregulation, behaviors of feedforward loops, and a unified Hill-function logic framework. Explicit-delay modeling simplifies the phenomenology of biological networks and may aid in discovering new functional motifs.
NATURE COMMUNICATIONS
(2021)