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
Biotechnology & Applied Microbiology
I. M. Serrano-Leon, P. Prieto, M. Aguilar
Summary: This study provides a comprehensive molecular analysis of telomeres and subtelomeres in barley chromosomes. The findings suggest that these regions play a significant role in the early chromosomal interactions during meiosis in barley, specifically in the homologous recognition and pairing process. Understanding the genome organization of barley and its role in plant breeding is crucial.
Article
Biochemistry & Molecular Biology
Denisa Komurkova, Alena Svobodova Kovarikova, Eva Bartova
Summary: G-quadruplexes (G4s) are primarily located in GC-rich regions and demonstrate high colocalization with transcription and splicing-related nuclear compartments such as nucleoli and nuclear speckles. Despite the lack of impact from RNAP II inhibitor and gamma-ray irradiation on the relationship between G4s and DNA damage foci, G4s still exhibit high stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Weibing Wang, Lin Gao, Yusen Ye, Yong Gao
Summary: The study proposes a two-stage random forest-based machine learning method, CTCF-mediated Chromatin Interaction Prediction (CCIP), to predict CTCF-mediated chromatin loops. Experimental results demonstrate that the method predicts CTCF-mediated loops more accurately than other methods and that transitivity, when used as a properly defined attribute, is informative for predicting CTCF loops. This work contributes to the understanding of the formation mechanism and function of CTCF-mediated chromatin loops.
Article
Multidisciplinary Sciences
Daniel J. Emerson, Peiyao A. Zhao, Ashley L. Cook, R. Jordan Barnett, Kyle N. Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltan Simandi, Miriam K. Minsk, Katelyn R. Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, Sergey V. Venev, Johan H. Gibcus, Hongbo Yang, Takayo Sasaki, Masato T. Kanemaki, Feng Yue, Job Dekker, Chun-Long Chen, David M. Gilbert, Jennifer E. Phillips-Cremins
Summary: This article reveals the determinants of replication origin positioning in the human genome. The study found that topologically associating domains and loops play crucial roles in the localization of replication initiation zones. By disrupting cohesin-mediated loop extrusion, the positioning of replication origins can be altered. These findings contribute to a better understanding of the mechanism of DNA replication.
Article
Immunology
Olivier Papapietro, Sergey Nejentsev
Summary: TOP2B plays a crucial role in transcription regulation and maintaining genome organization by unwinding DNA structures. Deficiency of TOP2B may lead to developmental defects in B-cell progenitors.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Laura Martin, Maria Victoria Neguembor, Maria Pia Cosma
Summary: One of the biggest paradoxes in biology is the disparity in size between the human genome and the nucleus that contains it. Despite being approximately 2 meters long, the DNA must be compacted and accessible for replication and transcription. The role of DNA torsional stress as a regulator of chromatin compaction and accessibility is discussed, with a focus on the influence of topoisomerases on genome organization.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Constanze Pentzold, Miriam Kokal, Stefan Pentzold, Anja Weise
Summary: Chromosomal fragile sites, positioned in the interphase nucleus with anchoring points at the nuclear lamina, exhibit fragility in mitosis but actually start in interphase, influencing genomic integrity and sustaining cellular diversity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
Summary: Chromosome structures vary between different cell types and regions, and are influenced by factors such as epigenetic state.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tom van Schaik, Stefano G. Manzo, Athanasios E. Vouzas, Ning Qing Liu, Hans Teunissen, Elzo de Wit, David M. Gilbert, Bas van Steensel
Summary: Through studying human cell lines, researchers have discovered that Ki-67 is associated with large genomic domains, particularly those involved in late DNA replication. The distribution pattern of Ki-67 on chromosomes varies throughout different stages of the cell cycle. These findings highlight the important roles that Ki-67 plays in genome interactions and heterochromatin organization.
Review
Cell Biology
A. K. Balaji, Santam Saha, Shruti Deshpande, Darshini Poola, Kundan Sengupta
Summary: Dysregulation of chromatin remodeling and nuclear envelope proteins plays a significant role in cancer development. Recent advances in single-cell sequencing, imaging technologies, and data mining approaches enable the design of small molecules to selectively inhibit cancer cell growth and proliferation in a genome- and epigenome-specific manner.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Alessandro Bertero
Summary: Research on three-dimensional genome organization has revealed the importance of both intra-chromosomal chromatin folding and inter-chromosomal chromatin interactions in gene regulation. While the latter has been traditionally overlooked, emerging evidence suggests that cross-chromosomal interactions play crucial roles in epigenetic control, transcription, and splicing. This highlights a potentially pervasive functional mechanism in biology where co-regulated nucleic acids are in close 3D proximity.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Florian Geiger, Julia Acker, Guido Papa, Xinyu Wang, William E. Arter, Kadi L. Saar, Nadia A. Erkamp, Runzhang Qi, Jack Pk Bravo, Sebastian Strauss, Georg Krainer, Oscar R. Burrone, Ralf Jungmann, Tuomas P. J. Knowles, Hanna Engelke, Alexander Borodavka
Summary: RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. The replication factories of rotaviruses represent protein-RNA condensates that can be reversibly dissolved by specific substances, impacting viral replication. These condensates exhibit different properties at different stages of viral infection, providing new insights into viral replication research.
Article
Computer Science, Interdisciplinary Applications
Felix Ocker, Birgit Vogel-Heuser, Christiaan J. J. Paredis
Summary: This paper presents a framework for automatically merging the reusable terminological components of production ontologies. By combining translations, domain-specific vocabularies, and inconsistency checks with syntactic, terminological, and structural analyses, the framework integrates formalized knowledge representations to improve support systems for engineers and enable unambiguous communication in smart factories.
COMPUTERS IN INDUSTRY
(2022)
Article
Plant Sciences
Richard B. Flavell
Summary: Epistatic interactions and negative heterosis in wheat have been found to be associated with interchromosomal interactions. Recent studies have produced a genome-wide atlas of functionally paired, interacting regulatory elements and genes in wheat. The integration of these studies provides new perspectives for wheat breeding and enhancing traits.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Reynand Jay Canoy, Franck Andre, Anna Shmakova, Joelle Wiels, Marc Lipinski, Yegor Vassetzky, Diego Germini
Summary: This article presents a novel and efficient protocol for transfection of B-cell lines and B cells from PBMCs, which are notoriously difficult to transfect. The protocol does not require expensive equipment or reagents and achieves high transfection and viability rates through optimization of salt concentration in the transfection medium and plasmid amount. The validation experiment of generating a TP53(-/-) RPMI8866 lymphoblastoid cell line demonstrates the potential applicability of this method in hematological and blood cancer studies.
Article
Biochemistry & Molecular Biology
Vlada V. Zakharova, Mikhail D. Magnitov, Laurence Del Maestro, Sergey Ulianov, Alexandros Glentis, Burhan Uyanik, Alice Williart, Anna Karpukhina, Oleg Demidov, Veronique Joliot, Yegor S. Vassetzky, Rene-Marc Mege, Matthieu Piel, Sergey Razin, Slimane Ait-Si-Ali
Summary: Imbalance in the system of chromatin-modifying enzymes is a hallmark of diseases such as cancer, as it affects the epigenome and transcriptional reprogramming. This study demonstrates that a loss-of-function mutation in the histone lysine methyltransferase SETDB1 leads to changes in the overall structure and mechanical properties of the nucleus in lung cancer cells, due to genome-wide redistribution of heterochromatin. This perturbs the spatial compartmentalization of chromatin and results in the reversed oncogenic potential of lung adenocarcinoma cells.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Sergey V. Razin, Omar L. Kantidze
Summary: The development of 'C-methods' has started a new era in 3D genome studies, allowing for the analysis of spatial contacts between distant genomic elements. Over the decades, the concept of spatial genome organization has evolved, and current views on the 3D genome and cell nucleus organization are being discussed. The inter-relation between gene regulation and the 3D genome is supported by experimental evidence.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Letter
Oncology
Anna Shmakova, Nikolai Lomov, Vladimir Viushkov, Tatyana Tsfasman, Yana Kozhevnikova, Darina Sokolova, Vadim Pokrovsky, Marina Syrkina, Diego Germini, Mikhail Rubtsov, Yegor Vassetzky
CANCER COMMUNICATIONS
(2023)
Editorial Material
Oncology
Anna Shmakova, Yegor Vassetzky
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Biochemical Research Methods
Victoria A. Kobets, Sergey Ulianov, Aleksandra A. Galitsyna, Semen A. Doronin, Elena A. Mikhaleva, Mikhail S. Gelfand, Yuri Y. Shevelyov, Sergey Razin, Ekaterina E. Khrameeva
Summary: The study introduces a novel approach called HiConfidence, which effectively eliminates technical biases from Hi-C data for more accurate analysis of genome structure changes and meaningful biological conclusions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Ekaterina P. P. Kalabusheva, Anastasia S. S. Shtompel, Alexandra L. L. Rippa, Sergey V. V. Ulianov, Sergey V. V. Razin, Ekaterina A. A. Vorotelyak
Summary: Keratins are specific intermediate filament-forming proteins found in epithelial cells. Their expression profiles change in different biological conditions, such as cell differentiation, injury, and malignant transformation. The tight regulation of keratin expression suggests the presence of complex regulatory mechanisms at the genomic level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Genetics & Heredity
Sergey V. Razin, Sergey V. Ulianov, Olga V. Iarovaia
Summary: In this review, the functioning of enhancers in the 3D genome is considered. The mechanisms of enhancer-promoter communication and the significance of their spatial proximity in the nuclear space are discussed. The review also presents a model of an activator chromatin compartment which allows for the transfer of activating factors from an enhancer to a promoter without direct contact.
Article
Biochemistry & Molecular Biology
Daniil A. A. Chernyavskij, Olga Yu. Pletjushkina, Anastasia V. V. Kashtanova, Ivan I. I. Galkin, Anna Karpukhina, Boris V. V. Chernyak, Yegor S. S. Vassetzky, Ekaterina N. N. Popova
Summary: Many muscular pathologies involving oxidative stress and elevated TNF levels cause muscle protein catabolism and impair myogenesis. This study found that mitoROS play a role in this process by triggering and enhancing mitophagy during myogenesis. Treatment with TNF before myogenesis decreases myoblast fusion and MYH2 synthesis, but antioxidants and autophagy suppression can partially restore myogenesis.
Article
Biology
Alexey A. Gavrilov, Grigory S. Evko, Aleksandra A. Galitsyna, Sergey V. Ulianov, Tatiana V. Kochetkova, Alexander Y. Merkel, Alexander V. Tyakht, Sergey V. Razin
Summary: Using the RedC RNA-DNA proximity ligation approach, we found that mRNA preferentially interacts with its cognate genes and downstream genes in the same operon, while ribosomal RNA shows a preference for interaction with active protein-coding genes. Additionally, the negative regulator 6S noncoding RNA is depleted from active genes in E. coli and B. subtilis. These findings provide valuable insights into prokaryotic gene expression and the role of noncoding RNAs.
COMMUNICATIONS BIOLOGY
(2023)
Review
Cell Biology
Olga Klaudia Szewczyk-Roszczenko, Piotr Roszczenko, Anna Shmakova, Nataliya Finiuk, Serhii Holota, Roman Lesyk, Anna Bielawska, Yegor Vassetzky, Krzysztof Bielawski
Summary: Endocytosis is a major cellular communication process that can be hijacked by pathogens and involved in oncogenic transformation. This review explores different approaches to inhibit endocytosis, discusses chemical inhibitors, and explores potential clinical applications.
Article
Microbiology
Ignat V. Sonets, Nikita V. Dovidchenko, Sergey V. Ulianov, Maria S. Yarina, Stanislav I. Koshechkin, Sergey V. Razin, Larissa M. Krasnopolskaya, Alexander V. Tyakht
Summary: The complete genome sequence of G. lucidum strain 5.1 was obtained using high-throughput shotgun sequencing. The improved assembly process resulted in 12 chromosome-level scaffolds. Comprehensive annotation of the genome identified genes likely involved in polysaccharide biosynthesis. This study is important for elucidating the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and understanding fungal genomic organization.
Article
Biochemistry & Molecular Biology
Reynand Jay Canoy, Anna Shmakova, Anna Karpukhina, Nikolai Lomov, Eugenia Tiukacheva, Yana Kozhevnikova, Franck Andre, Diego Germini, Yegor Vassetzky
Summary: Most cancer-related chromosomal translocations appear to be specific to certain cell types. However, our study shows that any translocation can potentially arise in any type of cell, and the frequency of translocation is correlated with the spatial proximity between gene loci after double-strand break induction. Furthermore, only specific translocations persisted after long-term culture.
Article
Biochemistry & Molecular Biology
Irina V. Zhegalova, Petr A. Vasiluev, Ilya M. Flyamer, Anastasia S. Shtompel, Eugene Glazyrina, Nadezda Shilova, Marina Minzhenkova, Zhanna Markova, Natalia V. Petrova, Erdem B. Dashinimaev, Sergey V. Razin, Sergey V. Ulianov
Summary: Trisomy refers to the presence of an extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies can have severe developmental abnormalities and affect various organs and systems. This study used high-throughput chromosome conformation capture technique to investigate the 3D chromatin structure in cells with trisomy 13, 16, and 18. The presence of extra chromosomes led to changes in contact frequencies between small and large chromosomes, and certain chromosomes showed stochastic changes in contact patterns. The compacted regions in trisomic cells were enriched in housekeeping genes, suggesting a decrease in chromatin accessibility and transcription level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Meeting Abstract
Cell & Tissue Engineering
O. Serbina, E. Kiseleva, Y. Vassetzky