Article
Biology
Evgeniya N. Andreyeva, Alexander Emelyanov, Markus Nevil, Lu Sun, Elena Vershilova, Christina A. Hill, Michael-C Keogh, Robert J. Duronio, Arthur Skoultchi, Dmitry Fyodorov
Summary: Asynchronous replication of chromosome domains during S phase is essential for genome function, but the mechanisms establishing early versus late replication domains in different cell types remain incompletely understood. A study in Drosophila found that the complex SUMM4, composed of SUUR and Mod(Mdg4)-67.2, can delay the replication of intercalary heterochromatin by attenuating the progression of replication forks, thereby implicating a chromatin barrier in replication control.
Editorial Material
Biochemistry & Molecular Biology
Ilona Faustova, Mart Loog
Summary: Study by Hossain et al. (2021) reveals that ORC1 and CDC6 interact during pre-replicative complex formation in G1, mediated by SLiMs in IDRs and regulated by CDKs.
Article
Multidisciplinary Sciences
Jose Mariano Amabis, Eduardo Gorab
Summary: This study focuses on the micronucleoli structures in the nucleoli of salivary gland nuclei of dipterans representative of Sciaridae, revealing a phenomenon of extreme nucleolar fragmentation/dispersion limited to specific cell types undergoing polyteny. The findings suggest that the transcriptional activity is present in almost all micronucleolar bodies generated in the salivary gland, indicating a process to counterbalance the rDNA loss due to under-replication. Furthermore, the chromosomal distribution of epigenetic markers demonstrates a role of heterochromatin in establishing rDNA topology in polytene nuclei of Sciaridae.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Zeeshan Abbas, Mobeen Ur Rehman, Hilal Tayara, Kil To Chong
Summary: In this article, a unique artificial intelligence-based technique called ORI-Explorer is developed to recognize origins of replication sites (ORIs) in four different eukaryotic species. ORI-Explorer combines multiple feature engineering techniques and utilizes the CatBoost Classifier. It outperforms existing predictors and provides key insights into model success through the SHapley Additive exPlanation method. ORI-Explorer aims to aid community-wide efforts in discovering potential ORIs and developing verifiable biological hypotheses.
Article
Cell Biology
Shin-ichiro Takebayashi, Tyrone Ryba, Kelsey Wimbish, Takuya Hayakawa, Morito Sakaue, Kenji Kuriya, Saori Takahashi, Shin Ogata, Ichiro Hiratani, Katsuzumi Okumura, Masaki Okano, Masato Ogata
Summary: Multiple epigenetic pathways, including DNA methylation, influence DNA replication timing. Loss of Dnmts has complex and diverse effects on the mammalian DNA replication landscape, with subtle but reproducible changes observed in various genomic regions. Replication timing in pericentromeric heterochromatin is correlated with redistribution of H3K27me3 induced by DNA hypomethylation.
Editorial Material
Biochemistry & Molecular Biology
Jason A. Halliwell, Eva R. Hoffmann
Summary: The study reveals evolutionary conservation between replication timing and meiotic recombination in males through mapping replication origins directly in mammalian tissue for the first time. This provides new insights into understanding germ cell formation.
Review
Biochemistry & Molecular Biology
Yanduo Zhang, Kailong Hou, Jinkai Tong, Haonan Zhang, Mengjie Xiong, Jing Liu, Shuting Jia
Summary: This review provides a comprehensive overview of the current findings on the regulation of ALT by Shelterin components, aiming to enhance the understanding of altered functions of Shelterin components in ALT cells and to identify potential targets for the treatment of ALT tumor cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lilas Courtot, Elodie Bournique, Chrystelle Maric, Laure Guitton-Sert, Miguel Madrid-Mencia, Vera Pancaldi, Jean-Charles Cadoret, Jean-Sebastien Hoffmann, Valerie Bergoglio
Summary: This study reveals that low replication stress can lead to advanced DNA replication timing, which is cell-type specific and involves large heterochromatin domains. These advanced events can be inherited by the next generation of cells, leading to changes in chromatin accessibility, replication origin landscape, and gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Deepak Bhat, Samuel Hauf, Charles Plessy, Yohei Yokobayashi, Simone Pigolotti, Armita Nourmohammad
Summary: In this study, a new method was proposed to infer the dynamics of Replisomes from DNA abundance distribution. The method was applied to measure the DNA abundance distribution in Escherichia coli populations growing at different temperatures. The results showed that the speed of Replisomes increases with temperature and exhibits wave-like variations along the genome, which correlates with the variation of mutation rate. This study provides insights into the replication dynamics of bacteria.
Editorial Material
Biochemistry & Molecular Biology
Gergely Rona, Michele Pagano
Summary: Cells prevent rereplication by avoiding licensing of neosynthesized DNA. In this study published in Molecular Cell, Ratnayeke et al. (2022)(1) demonstrate that the licensing factor CDT1 inhibits CMG helicase progression at replication forks by suppressing DNA elongation before its degradation.
Editorial Material
Genetics & Heredity
Cristian Polo Rivera, Tom D. Deegan
Summary: Repliconseq is a new genome-wide DNA sequencing technology introduced by Claussin et al. that enables high-resolution monitoring of individual replisomes in vivo.
TRENDS IN GENETICS
(2022)
Editorial Material
Cell Biology
Jean-Sebastien Hoffmann
Summary: The major challenge in DNA replication is to ensure the transmission of intact genetic material to daughter cells. Despite extensive research on the cellular responses to replication problems and their source, the transmission of genome modifications and their heritability in mitosis has been less documented. Recent studies have shown that low replication stress can impact the next generation of cells, transmitting DNA damage and altering the replication timing program of chromosomal domains in daughter cells. This progression of replication issues into mitosis and daughter cells may provide advantages by alerting cells to risky loci and offering an adaptive mechanism to anticipate future problems, especially in the context of cancer cell resistance to therapy.
Review
Cell Biology
Marina A. Bellani, Althaf Shaik, Ishani Majumdar, Chen Ling, Michael M. Seidman
Summary: The replication apparatus faces challenges in duplicating the genome, particularly when encountering covalent DNA adducts on the leading template strand. The helicase, a key component of the replication machinery, is responsible for unwinding DNA and coming into contact with the adducts. Recent studies have shown that the helicase is able to tolerate larger adducts than previously believed.
Review
Biochemistry & Molecular Biology
Joanna Morcinek-Orlowska, Karolina Zdrojewska, Alicja Wegrazyn
Summary: DNA polymerases are enzymes that synthesize DNA and play important roles in DNA replication, repair, and genetic recombination. Phage-encoded DNA polymerases exhibit unique structural and functional properties, which are crucial for the survival of these viruses and can also be utilized in genetic engineering and biotechnology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mary E. Anderson, Janet L. Smith, Alan D. Grossman
Summary: DNA replication is regulated primarily at the initiation step, where DnaA and oriC are the key targets. Multiple mechanisms including elongation and initiation can compensate for over-initiation, highlighting the complexity of replication regulation.
MOLECULAR MICROBIOLOGY
(2022)
Article
Immunology
Lili Jing, Owen J. Tamplin, Michael J. Chen, Qing Deng, Shenia Patterson, Peter G. Kim, Ellen M. Durand, Ashley McNeil, Julie M. Green, Shinobu Matsuura, Julien Ablain, Margot K. Brandt, Thorsten M. Schlaeger, Anna Huttenlocher, George Q. Daley, Katya Ravid, Leonard I. Zon
JOURNAL OF EXPERIMENTAL MEDICINE
(2015)
Article
Veterinary Sciences
Shinpei Kawarai, Masaharu Hisasue, Shinobu Matsuura, Tetsuro Ito, Yukari Inoue, Sakurako Neo, Yoko Fujii, Hiroo Madarame, Kinji Shirota, Ryo Tsuchiya
JOURNAL OF THE AMERICAN ANIMAL HOSPITAL ASSOCIATION
(2015)
Article
Hematology
Shinobu Matsuura, Rongjuan Mi, Milka Koupenova, Alexia Eliades, Shenia Patterson, Paul Toselli, Jonathan Thon, Joseph E. Italiano, Philip C. Trackman, Nikolaos Papadantonakis, Katya Ravid
Article
Oncology
S. Weng, S. Matsuura, C. T. Mowery, S. A. Stoner, K. Lam, D. Ran, A. G. Davis, M-C Lo, D-E Zhang
Letter
Oncology
S. Matsuura, S. Patterson, H. Lucero, O. Leiva, A. K. Grant, V. L. M. Herrera, K. Ravid
BLOOD CANCER JOURNAL
(2016)
Letter
Oncology
K. Lam, A. Muselman, R. Du, M. Yan, S. Matsuura, D-E Zhang
BLOOD CANCER JOURNAL
(2016)
Article
Cell Biology
Moshe Shashar, Mostafa E. Belghasem, Shinobu Matsuura, Joshua Walker, Sean Richards, Faisal Alousi, Keshab Rijal, Vijaya B. Kolachalama, Mercedes Balcells, Minami Odagi, Kazuo Nagasawa, Joel M. Henderson, Amitabh Gautam, Richard Rushmore, Jean Francis, Daniel Kirchhofer, Kumaran Kolandaivelu, David H. Sherr, Elazer R. Edelman, Katya Ravid, Vipul C. Chitalia
SCIENCE TRANSLATIONAL MEDICINE
(2017)
Review
Oncology
O. Leiva, S. K. Ng, S. Chitalia, A. Balduini, S. Matsuura, K. Ravid
BLOOD CANCER JOURNAL
(2017)
Article
Urology & Nephrology
Vijaya B. Kolachalama, Moshe Shashar, Faisal Alousi, Sowmya Shivanna, Keshab Rijal, Mostafa E. Belghasem, Joshua Walker, Shinobu Matsuura, Gary H. Chang, C. Michael Gibson, Laura M. Dember, Jean M. Francis, Katya Ravid, Vipul C. Chitalia
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2018)
Article
Hematology
Shinobu Matsuura, Cristal Reyna Thompson, Seng Kah Ng, Christina Marie Ward, Aikaterini Karagianni, Carla Mazzeo, Alessandro Malara, Alessandra Balduini, Katya Ravid
Review
Hematology
Xiaosheng Yang, Shlok V. Chitalia, Shinobu Matsuura, Katya Ravid
Summary: This review discusses the different integrins expressed on bone marrow megakaryocytes and their roles in lineage development and cellular functions, such as cell adhesion and proplatelet formation. The review also reviews the pathologies associated with dysregulated megakaryocyte integrin expression.
EXPERIMENTAL HEMATOLOGY
(2022)
Article
Biochemical Research Methods
Maissa M. M. Gaye, Christina M. M. Ward, Andrew J. J. Piasecki, Vanessa L. L. Stahl, Aikaterini Karagianni, Catherine E. E. Costello, Katya Ravid
Summary: This study found that the JAK2V617F mutation leads to changes in glycosylation, particularly in the beta 1 integrin, in patients with primary myelofibrosis. The glycosylation changes in alpha 2 integrin were more substantial and may also affect activation. The methodology employed in this study has the potential to provide insights into the consequences of integrin activation in MKs at the peptide level.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Letter
Hematology
Vittorio Abbonante, Vipul Chitalia, Vittorio Rosti, Orly Leiva, Shinobu Matsuura, Alessandra Balduini, Katya Ravid