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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)
Editorial Material
Biochemistry & Molecular Biology
Zhiming Li, Zhiguo Zhang
Summary: Histone chaperones play important roles in the biogenesis, transportation, and deposition of histones, affecting processes such as DNA replication, transcription, and epigenetic inheritance. In this study, Carraro et al. uncover an interconnected chaperone network and discover a surprising function of the histone chaperone DAXX in de novo deposition of H3.3K9me3.
Review
Biochemistry & Molecular Biology
Celine Duc, Christophe Thiriet
Summary: The review focuses on the remodeling of chromatin during DNA replication in the S-phase, including the eviction of nucleosomes and the assembly of newly synthesized histones. The recycling of parental histones and the nuclear import of histones are also discussed in relation to epigenetic inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Yehudit Bergman, Itamar Simon, Howard Cedar
Summary: Developmental programming involves a sequence of molecular choices that epigenetically mark the genome to generate stable cell types in the organism. Asynchronous replication timing (ASRT) may serve as a sophisticated universal mechanism for mediating and maintaining crucial decisions in biological processes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Liudmila Popova, Prabakaran Nagarajan, Callie M. Lovejoy, Benjamin D. Sunkel, Miranda L. Gardner, Meng Wang, Michael A. Freitas, Benjamin Z. Stanton, Mark R. Parthun
Summary: In this study, it was found that the loss of HAT1 during replication resulted in inaccessibility of specific heterochromatin regions, which make up a significant portion of the genome. Additionally, HAT1 was shown to have a global repression effect on H3 K9 me3 levels and overlap with a subset of Lamin-Associated Domains.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Stefano Gnan, Ilya M. Flyamer, Kyle N. Klein, Eleonora Castelli, Alexander Rapp, Andreas Maiser, Naiming Chen, Patrick Weber, Elin Enervald, M. Cristina Cardoso, Wendy A. Bickmore, David M. Gilbert, Sara C. B. Buonomo
Summary: The study reveals the dual role of RIF1 as a chromatin interaction scaffold and regulator of replication timing in coordinating nuclear architecture and the replication-timing programme, showing that these two processes are interdependent.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Lina-Marie Briu, Chrystelle Maric, Jean-Charles Cadoret
Summary: The replication-timing program is crucial in eukaryotic nuclear processes and is closely linked to transcriptional activity, epigenetic landscape, and the 3D organization of the genome. There is a complex relationship between replication timing, replication stress, and genomic instability, although the extent of their mutual connection requires further investigation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Matthew W. Parker, Jonchee A. Kao, Alvin Huang, James M. Berger, Michael R. Botchan
Summary: Researchers demonstrate that phase separation is driven by a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts, dependent on sequence composition but not order. These interactions are resistant to 1,6-hexanediol and independent of aromaticity, revealing distinct mechanisms underlying condensate formation and specificity in different phase-separating systems.
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Biochemistry & Molecular Biology
Yue Wang, Yunchao Huang, Edith Cheng, Xinhua Liu, Yu Zhang, Jianguo Yang, Jordan T. F. Young, Grant W. Brown, Xiaohan Yang, Yongfeng Shang
Summary: This study reveals an unexpected role for lysine-specific demethylase 1 (LSD1) in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. The findings support the potential use of selective inhibitors of LSD1 in cancer therapy, while emphasizing the need to maintain an appropriate level of LSD1 to minimize side effects.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Genetics & Heredity
Logan Richards, Souradip Das, Jared T. Nordman
Summary: Successful and accurate replication of the genome is crucial for maintaining genomic stability and preventing diseases. Replication timing (RT), which determines when each segment of the genome is replicated, is an important aspect of genome duplication. The protein Rif1 plays a key role in regulating RT, by delaying the activation of helicase in certain regions of the genome. However, many questions still remain regarding the mechanisms of Rif1 function.
Article
Multidisciplinary Sciences
Alexa N. Bracci, Anissa Dallmann, Qiliang Ding, Melissa J. Hubisz, Madison Caballero, Amnon Koren
Summary: Replication timing of DNA is linked to gene regulation and genome stability. The differences in replication timing between humans and chimpanzees suggest ongoing evolution of the DNA replication timing program. These differences are driven by DNA sequence alterations and can impact gene expression and chromatin structure.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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Cell Biology
Caitlin Connolly, Saori Takahashi, Hisashi Miura, Ichiro Hiratani, Nick Gilbert, Anne D. Donaldson, Shin-Ichiro Hiraga
Summary: The organization of chromatin is important for chromosomal activities. SAF-A protein plays a crucial role in promoting DNA replication and maintaining its progression. Depletion of SAF-A results in reduced origin licensing, inconsistent replication forks, and changes in replication timing.
JOURNAL OF CELL SCIENCE
(2022)
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Evolutionary Biology
Michael E. Goldberg, Kelley Harris
Summary: The mutation spectra of great apes differ across genomic regions and are not driven by specific functional compartments. Additionally, many compartments have their own characteristic mutational signatures that remain stable throughout the great ape phylogeny.
GENOME BIOLOGY AND EVOLUTION
(2022)
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Cell Biology
Nicholas A. Pease, Phuc H. B. Nguyen, Marcus A. Woodworth, Kenneth K. H. Ng, Blythe Irwin, Joshua C. Vaughan, Hao Yuan Kueh
Summary: This study elucidates an epigenetic switch controlling the T cell commitment gene Bcl11b, which holds its locus in an heritable inactive state for multiple cell generations before activation. The mechanism involves regulating H3K27me3 levels at Bcl11b by methyltransferase and demethylase activities, setting a time delay for the locus to switch from a silent state to an active state. This activation delay is robustly tunable by chromatin modifiers and transcription factors, spanning many cell generations and independent of cell division, suggesting potential broad control over timing in development.
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Biology
Roman Jaksik, David A. A. Wheeler, Marek Kimmel
Summary: This study proposes a method of detecting ORI based on somatic mutation patterns caused by the mutator phenotype of damaged DNA polymerase epsilon (POLE), and identifies shared ORI locations in tumors through accumulated mutations. The study also compares the results from multiple detection methods and defines a consensus set of ORI. The results demonstrate the viability of mutation-based detection in determining ORI location and associated sequence features.
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Multidisciplinary Sciences
Benjamin S. Freedman, Craig R. Brooks, Albert Q. Lam, Hongxia Fu, Ryuji Morizane, Vishesh Agrawal, Abdelaziz F. Saad, Michelle K. Li, Michael R. Hughes, Ryan Vander Werff, Derek T. Peters, Junjie Lu, Anna Baccei, Andrew M. Siedlecki, M. Todd Valerius, Kiran Musunuru, Kelly M. McNagny, Theodore I. Steinman, Jing Zhou, Paul H. Lerou, Joseph V. Bonventre
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Wenzhang Wang, Luwen Wang, Junjie Lu, Sandra L. Siedlak, Hisashi Fujioka, Jingjing Liang, Sirui Jiang, Xiaopin Ma, Zhen Jiang, Edroaldo Lummertz da Rocha, Max Sheng, Heewon Choi, Paul H. Lerou, Hu Li, Xinglong Wang
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Cell & Tissue Engineering
Junjie Lu, Hu Li, Anna Baccei, Takayo Sasaki, David M. Gilbert, Paul H. Lerou
STEM CELLS AND DEVELOPMENT
(2016)
Letter
Critical Care Medicine
Ruggero Spadafora, Junjie Lu, Radhika S. Khetani, Cheng Zhang, Aimee Iberg, Hu Li, Yang Shi, Paul H. Lerou
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2018)
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Cell Biology
Junjie Lu, David M. Gilbert
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Cell Biology
Lchiro Hiratani, Shin-ichiro Takebayashi, Junjie Lu, David M. Gilbert
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2009)
Article
Biochemistry & Molecular Biology
Tyrone Ryba, Ichiro Hiratani, Junjie Lu, Mari Itoh, Michael Kulik, Jinfeng Zhang, Thomas C. Schulz, Allan J. Robins, Stephen Dalton, David M. Gilbert
Correction
Cell Biology
Junjie Lu, David M. Gilbert
JOURNAL OF CELL BIOLOGY
(2008)
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Multidisciplinary Sciences
Bryan R. Gorman, Junjie Lu, Anna Baccei, Nathan C. Lowry, Jeremy E. Purvis, Rami S. Mangoubi, Paul H. Lerou
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Multidisciplinary Sciences
Tomoki Yokochi, Kristina Poduch, Tyrone Ryba, Junjie Lu, Ichiro Hiratani, Makoto Tachibana, Yoichi Shinkai, David M. Gilbert
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2009)
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Cell Biology
Junjie Lu, Hu Li, Ming Hu, Takayo Sasaki, Anna Baccei, David M. Gilbert, Jun S. Liu, James J. Collins, Paul H. Lerou
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Cell Biology
Junjie Lu, David M. Gilbert
JOURNAL OF CELL BIOLOGY
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Biochemistry & Molecular Biology
ZW Tang, YJ Zhao, F Mei, SM Yang, X Li, JJ Lv, L Hou, B Zhang
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2004)
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Biochemistry & Molecular Biology
JJ Lv, HJ Liu, QA Wang, ZW Tang, L Hou, B Zhang
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(2003)