Article
Biochemistry & Molecular Biology
Zilong Li, Tamar Schlick
Summary: This article presents a method called Hi-BDiSCO that generates 3D genome structures from Hi-C and Micro-C data using a mesoscale-resolution chromatin model based on the DiSCO model. By integrating reconstruction with nucleosome resolution chromatin simulations, the method is applied to different gene contexts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Bin-Bin Xie, Jin-Cheng Rong, Bai-Lu Tang, Sishuo Wang, Guiming Liu, Qi-Long Qin, Xi-Ying Zhang, Weipeng Zhang, Qunxin She, Yin Chen, Fuchuan Li, Shengying Li, Xiu-Lan Chen, Haiwei Luo, Yu-Zhong Zhang
Summary: Chromosome replication is essential for cell division, with bidirectional replication being the rule for bacterial chromosomes. In Pseudoalteromonas, chromids can replicate either unidirectionally or bidirectionally, indicating a single evolutionary transition from unidirectionality to bidirectionality. This study sheds light on the physiological aspects of chromosome replication and the early evolutionary history of bacterial chromosomes.
Article
Biology
Julian Haase, Richard Chen, Wesley M. Parker, Mary Kate Bonner, Lisa M. Jenkins, Alexander E. Kelly
Summary: The TFIIH complex plays a crucial role in maintaining chromosome compaction and condensin enrichment by dynamically altering the chromatin environment to facilitate condensin loading and condensin-dependent loop extrusion.
Article
Biology
Martin Houlard, Erin E. Cutts, Muhammad S. Shamim, Jonathan Godwin, David Weisz, Aviva Presser Aiden, Erez Lieberman Aiden, Lothar Schermelleh, Alessandro Vannini, Kim Nasmyth
Summary: The eukaryotic cell cycle is characterized by dramatic changes in chromosomal DNA morphology between interphase and mitosis. Cohesin and condensin enzymes extrude DNA loops to configure chromosomal DNA topology, with cohesin acting during interphase and condensin primarily during mitosis. MCPH1 gene mutations in patients with microcephaly and the deletion of Mcph1 in mouse embryonic stem cells unleash condensin II activity during interphase, leading to compact chromosomes in G1 and G2 phases. This process is inhibited by MCPH1's binding to condensin II's NCAPG2 subunit, highlighting the crucial role of MCPH1 in blocking condensin II's association with chromatin.
Article
Multidisciplinary Sciences
Hammam Antar, Young-Min Soh, Stefano Zamuner, Florian P. Bock, Anna Anchimiuk, Paolo De los Rios, Stephan Gruber
Summary: Three-component ParABS systems play important roles in plasmid partitioning and chromosome segregation in bacteria, with ParB acting as a crucial adaptor protein. CTP hydrolysis is essential for efficient chromosome segregation by ParABS, contributing to partition complex assembly through two mechanisms.
Review
Biochemistry & Molecular Biology
Fares Osam Yanez-Cuna, Romain Koszul
Summary: Chromosomes in all domains of life have well-defined structures and hierarchical organization. The regulation of this organization and its interplay with gene expression and other chromosome processes are actively studied. Bacterial chromosomes are gene-dense and organized into a nucleoid, a membraneless compartment composed of DNA, RNA, and proteins. Recent advances in imaging and genomic methods have improved our understanding of bacterial chromosomal organization.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Michael Mitter, Zsuzsanna Takacs, Thomas Koecher, Ronald Micura, Christoph C. H. Langer, Daniel W. Gerlich
Summary: This study presents a protocol for sister chromatid-sensitive Hi-C (scsHi-C) that allows investigation of the organization of replicated genomes. The scsHi-C technique distinguishes DNA contacts within individual sister chromatids from those between sister chromatids, enabling the mapping of 3D genome organization in replicated chromosomes. The protocol combines chromosome conformation capture with labeling of nascent DNA and has the potential to be applied in various cell types.
Article
Biotechnology & Applied Microbiology
A. Maslova, V. Plotnikov, M. Nuriddinov, M. Gridina, V. Fishman, A. Krasikova
Summary: This study analyzed the 3D genome organization and chromosome rearrangements in the LSCC-HD3 cell line using high-throughput chromosome conformation capture (Hi-C) technology. It revealed a severely rearranged karyotype in the HD3 cell line and provided insights into the genome structure-function relationships in avian models with a large number of microchromosomes.
Article
Cell Biology
Florian P. Bock, Hon Wing Liu, Anna Anchimiuk, Marie-Laure Diebold-Durand, Stephan Gruber
Summary: Cells have the remarkable ability to organize and segregate chromosomes, which involves the cooperation between SMC complexes and ParB proteins. This study demonstrates that the bacterial Smc complex, along with ParB, can function together to organize and segregate foreign chromosomes, shedding light on the mechanisms of chromosome folding and segregation.
Article
Chemistry, Physical
Abdul Wasim, Palash Bera, Jagannath Mondal
Summary: We developed an integrative model of E. coli chromosome, which combines multiresolution genome-wide experimental data to describe its conformation. The model generates an appropriate ensemble of conformations and exhibits key features of the E. coli chromosome, such as nonoverlapping macrodomains and plectonemic loops. It can predict a higher resolution contact probability map than previous experiments and demonstrate chromosome segregation in a partially replicating cell. The modular nature of the model allows us to quantify the individual role of key features in hierarchical organization of the bacterial chromosome.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Eugene Kim, Alejandro Martin Gonzalez, Biswajit Pradhan, Jaco van der Torre, Cees Dekker
Summary: Condensin is a motor protein that organizes chromosomes by extruding loops of DNA. This study investigates how DNA supercoiling affects loop extrusion and provides insights into the loading and formation of supercoiled loops by SMC complexes.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Joanna M. Wenda, Reinier F. Prosee, Caroline Gabus, Florian A. Steiner
Summary: Centromeres are crucial regions on chromosomes for kinetochore formation and microtubule attachment during mitosis. In the nematode C. elegans, the loading factor KNL-2 plays a key role in CENP-A deposition. Phosphorylation of KNL-2 by CDK-1 regulates the cooperation between centromeres and the condensation machinery, impacting chromosome segregation and condensation levels.
JOURNAL OF CELL SCIENCE
(2021)
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
Multidisciplinary Sciences
David Buhrke, Norbert Michael, Peter Hamm
Summary: Phytochromes are commonly found photoreceptor proteins that undergo secondary structure refolding in response to chromophoric group photoisomerization. Two-dimensional infrared absorption spectroscopy is used to study the photoreaction of bacterial phytochrome Agp1, showing that dipole coupling between the chromophore and the tongue region plays a role in stabilizing the protein in the light-activated state.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Anna Anchimiuk, Virginia S. Lioy, Florian Patrick Bock, Anita Minnen, Frederic Boccard, Stephan Gruber
Summary: SMC complexes are essential for organizing and segregating chromosomes, but the mechanism behind their movement along DNA remains largely unknown. Factors such as loading sites, residency time, translocation rate, and abundance of complexes influence bacterial chromosome organization by modulating the frequency of encounters between SMC complexes. Fine-tuned parameters help to reduce collisions and resolve them effectively.
Article
Biochemistry & Molecular Biology
Alan Koh, Marjorie J. Gibbon, Marc W. van der Kamp, Christopher R. Pudney, Susanne Gebhard
Summary: Bacteria tightly control gene expression to minimize fitness costs associated with antibiotic resistance. In Bacillus subtilis, a novel regulatory logic involving a two-component system and an ABC transporter allows direct monitoring of detoxification needs. The transporter not only activates the kinase, but also helps maintain its inactive state, ensuring precise flux-dependent signaling control. Transport flux-dependent signaling conserves energy and provides a unique strategy for energy-efficient decision making.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Etienne Routhier, Edgard Pierre, Ghazaleh Khodabandelou, Julien Mozziconacci
Summary: Genomics is widely used in current research, including modifying coding or non-coding regions to alter gene expression levels. Single nucleotide mutations can lead to unexpected changes in epigenetic regulation of genes. Deep learning methods can help predict the impact of mutations on chromatin, providing guidance for designing synthetic genomes.
Article
Biochemical Research Methods
Thomas Haschka, Loic Ponger, Christophe Escude, Julien Mozziconacci
Summary: Genomic sequences are commonly used to infer evolutionary history, with MNHN-Tree-Tools being a high-performance algorithm set for clustering and tree building. It does not rely on multiple sequence alignment, making it suitable for large datasets and various applications such as human alpha-satellite repeats classification and tree of life derivation from 16S/18S rDNA sequences.
Review
Biochemical Research Methods
Thomas Haschka, Jean Baptiste Morlot, Leopold Carron, Julien Mozziconacci
Summary: This article discusses how enhancement methods improve the performance of common distance measures, presents a systematic approach to evaluate the separability of experimental replicates, and shows that the application of the "contrast increasing mutual proximity" significantly enhances performance across various distance measures. Depending on the type of epigenetic experiment, the MP coupled with Pearson, Cosine, or other distances proves to be highly efficient in discriminating epigenomic profiles.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Simone Pelliciari, Mei-Jing Dong, Feng Gao, Heath Murray
Summary: Genome replication is essential for cell proliferation, and a basal mechanism for opening bacterial chromosome origins has been proposed recently. Core elements of this mechanism are predicted to be present in the majority of bacterial chromosome origins, indicating functional conservation and a potential ancestral system for opening bacterial chromosome origins.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Astrid Lancrey, Alexandra Joubert, Evelyne Duvernois-Berthet, Etienne Routhier, Saurabh Raj, Agnes Thierry, Marta Sigarteu, Loic Ponger, Vincent Croquette, Julien Mozziconacci, Jean-Baptiste Boule
Summary: The artificial 601 DNA sequence is effective in positioning nucleosomes in vitro, but its application in vivo is limited and depends on the chromosomal context.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Virology
Joao Diogo Dias, Nazim Sarica, Axel Cournac, Romain Koszul, Christine Neuveut
Summary: Viruses that transcribe their DNA within the nucleus have to adapt to cellular mechanisms governing transcriptional regulation. This review provides an updated overview of how hepatitis B virus interacts with the cellular 3D genome and its impact on viral and cellular gene expression. The strategies employed by other DNA viruses to manipulate cellular genome spatial organization are also briefly discussed.
Article
Biochemistry & Molecular Biology
Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Nicole Quenech'Du, Charlotte Cockram, Romain Koszul, Olivier Espeli
Summary: In bacteria, the decatenation activity of topoisomerase IV plays a crucial role in chromosome replication and segregation. This study reveals that inactivation of topoisomerase IV leads to massive chromosome reorganization and increased contacts between nearby and distant loci. The roles of Topo III, MatP, and MukB in this process were also investigated.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Nathalie Bastie, Christophe Chapard, Lise Dauban, Olivier Gadal, Frederic Beckouet, Romain Koszul
Summary: This study investigates the roles of various cohesin regulators in tuning chromatin loop expansion in budding yeast, revealing that Scc2 plays a key role in both stimulating cohesin ATPase activity and driving cohesin translocation on DNA, while Smc3 acetylation during S phase counteracts this activity by stabilizing Pds5 to finely tune loop size and stability in G2.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Peter L. Voyvodic, Ismael Conejero, Khouloud Mesmoudi, Eric Renard, Philippe Courtet, Diego Cattoni, Jerome Bonnet
Summary: Cell-free biosensors are promising tools for medical diagnostics, but their performance can be affected by matrix effects. This study systematically evaluated the performance and robustness of cell-free systems in different clinical samples and found that an RNase inhibitor can mitigate matrix effects. By designing a new strain, interference from glycerol in the commercial buffer was resolved and higher reporter levels were obtained.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Jonay Garcia-Luis, Helene Bordelet, Agnes Thierry, Romain Koszul, Luis Aragon
Summary: This study reveals that degradation of cohesin during anaphase onset leads to aberrant chromatid segregation in yeast cells. Hi-C analysis of segregating chromatids shows that depletion of cohesin results in loss of intrachromatid organization. Surprisingly, cleavage of cohesin through specific methods does not significantly disrupt chromatid organization during anaphase, explaining successful bulk segregation.
Article
Biochemistry & Molecular Biology
Charles Winterhalter, Daniel Stevens, Stepan Fenyk, Simone Pelliciari, Elie Marchand, Panos Soultanas, Aravindan Ilangovan, Heath Murray
Summary: This study reports both positive and negative mechanisms for directing helicase recruitment in the model organism Bacillus subtilis. By characterizing the initiation protein DnaD, distinct protein interfaces required for helicase loading were identified. The role of the repressor protein SirA in inhibiting helicase recruitment was also discovered, advancing our understanding of DNA replication initiation in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Charles Winterhalter, Simone Pelliciari, Daniel Stevens, Stepan Fenyk, Elie Marchand, Nora B. Cronin, Panos Soultanas, Tiago R. D. Costa, Aravindan Ilangovan, Heath Murray
Summary: This study investigated the DNA replication initiation protein DnaD in Bacillus subtilis and identified a new single-stranded DNA motif called DnaD Recognition Element (DRE) in oriC. Through cryo-electron microscopy imaging, it was proposed that the location of DRE orchestrates the strand-specific recruitment of helicase during DNA replication initiation.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Fares Osam Yanez-Cuna, Romain Koszul
Summary: Chromosomes in all domains of life have well-defined structures and hierarchical organization. The regulation of this organization and its interplay with gene expression and other chromosome processes are actively studied. Bacterial chromosomes are gene-dense and organized into a nucleoid, a membraneless compartment composed of DNA, RNA, and proteins. Recent advances in imaging and genomic methods have improved our understanding of bacterial chromosomal organization.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
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.
