Article
Biochemistry & Molecular Biology
Faye M. Vassel, Daniel J. Laverty, Ke Bian, Cortt G. Piett, Michael T. Hemann, Graham C. Walker, Zachary D. Nagel
Summary: Rev7 is a regulatory protein with multiple functions, including roles in TLS, DSB repair, replication fork protection, and cell cycle regulation. Dimerization of Rev7 is important for its roles in TLS, DSB repair, and regulation of the anaphase promoting complex, but partially dispensable for promoting mitotic spindle assembly through its interaction with Ran.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lisa Schubert, Ivo A. Hendriks, Emil P. T. Hertz, Wei Wu, Selene Selles-Baiget, Saskia Hoffmann, Keerthana Stine Viswalingam, Irene Gallina, Satyakrishna Pentakota, Bente Benedict, Joachim Johansen, Katja Apelt, Martijn S. Luijsterburg, Simon Rasmussen, Michael Lisby, Ying Liu, Michael L. Nielsen, Niels Mailand, Julien P. Duxin
Summary: This study reveals an essential role of SCAI in ensuring error-free ICL repair upon activation of the FA pathway. SCAI forms a complex with Pol zeta and localizes to ICLs during DNA replication. In the absence of SCAI, HR-mediated ICL repair is defective, resulting in deletions and radial chromosomes.
Article
Biochemistry & Molecular Biology
Xiaopeng Lu, Min Xu, Qian Zhu, Jun Zhang, Ge Liu, Yantao Bao, Luo Gu, Yuan Tian, He Wen, Wei-Guo Zhu
Summary: Histone methyltransferase KMT5A interacts with E3 ligases RNF8 and RNF168 to establish histone modification status for DNA damage repair. KMT5A increases H4K20 monomethylation at DSBs and enhances RNF168's activity in catalyzing H2A ubiquitination, linking the two processes. The interaction between H2A acidic patch and KMT5A residues R188/R189 is crucial for KMT5A-mediated regulation of H2A ubiquitination.
Article
Biochemistry & Molecular Biology
Shuwei Xie, Naava Naslavsky, Steve Caplan
Summary: Primary cilia are sensory organelles that coordinate diverse signaling pathways, controlling development and homeostasis. In this study, we found that EHD1 regulates the ubiquitination of CP110, a protein required for ciliogenesis, and identified HERC2 and MIB1 as E3 ubiquitin ligases that interact with and ubiquitinate CP110. We also discovered that HERC2 is necessary for ciliogenesis and localizes to centriolar satellites, which play a role in ciliogenesis regulation. Our findings highlight a mechanism in which EHD1 controls the movement of centriolar satellites and HERC2 to the mother centriole during ciliogenesis, promoting CP110 ubiquitination and degradation.
Review
Biochemistry & Molecular Biology
Joseph D. Kaszubowski, Michael A. Trakselis
Summary: High fidelity DNA polymerases are crucial for genome replication, but they can become stalled at damaged sites. Translesion synthesis polymerases can temporarily take over synthesis at these sites, but they are less accurate. Mechanisms are needed to recruit high fidelity polymerases back to ensure accurate synthesis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Siyi Zhang, Tingting Zhou, Zhuo Wang, Fei Yi, Chunlu Li, Wendong Guo, Hongde Xu, Hongyan Cui, Xiang Dong, Jingwei Liu, Xiaoyu Song, Liu Cao
Summary: Faithful DNA replication is crucial for cell survival and inheritance, but damage can lead to replication stalling and DNA lesions. Post-translational modifications of PCNA regulate DNA synthesis and damage tolerance to maintain genomic stability. Dysregulation of PCNA PTMs can result in DNA breaks, affecting cell response and causing mutations.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Pharmacology & Pharmacy
L. B. Volk, K. L. Cooper, T. Jiang, M. L. Paffett, L. G. Hudson
Summary: Arsenite inhibits translesion synthesis (TLS) by interfering with the function of DNA repair protein Rad18. This leads to the retention of UV-induced DNA damage and accumulation of replication stress. Arsenite also affects the activity and regulation of Rad18, inhibiting PCNA monoubiquitination and polymerase eta recruitment, thus enhancing the bypass of cyclobutane pyrimidine dimers. These effects result in increased levels of replication stress, single-stranded DNA gaps, and DNA double-strand breaks, which can potentially cause mutations and contribute to the cocarcinogenicity of arsenite.
TOXICOLOGY AND APPLIED PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thomas A. Guilliam, Joseph T. P. Yeeles
Summary: The study shows that a yeast replisome is inherently tolerant to the oxidative lesion Tg, efficiently bypassing leading-strand Tg even in the absence of TLS machinery. A switch from Pol epsilon to Pol delta after helicase-polymerase uncoupling promotes rapid, efficient, and error-free lesion bypass at physiological nucleotide levels. Replicase switching may facilitate continued leading-strand synthesis when Pol delta is more effective at bypassing damage than Pol epsilon.
Article
Biochemistry & Molecular Biology
Minakshi Sharma, Deepak T. Nair
Summary: Apicomplexans like Plasmodium falciparum possess a unique organelle called the apicoplast with its own genome, which is prone to oxidative stress. The enzyme Pfprex, specifically its polymerase module PfpPol, is responsible for replicating the apicoplast genome and can carry out translesion DNA synthesis past common DNA lesions caused by oxidative stress. Residues N505 and Y509 in PfpPol play a crucial role in lesion bypass capability.
Article
Multidisciplinary Sciences
Sabrina F. Mansilla, Agostina P. Bertolin, Sofia Venerus Arbilla, Bryan A. Castano, Tiya Jahjah, Jenny K. Singh, Sebastian O. Siri, Maria Victoria Castro, Maria Belen de la Vega, Annabel Quinet, Lisa Wiesmueller, Vanesa Gottifredi
Summary: Recent studies have shown that the choice of a DNA damage tolerance pathway involves competition between PrimPol-mediated repriming and fork reversal. Pol t plays a unique role in regulating this pathway choice, with Pol t deficiency leading to PrimPol-dependent repriming and accelerated DNA replication. However, this excessive participation of PrimPol in DNA elongation can trigger chromosome instability and replication stress signals in Pol t-depleted cells, revealing an unexpected role of Pol t in protecting genome stability.
Article
Biology
Chuanyang Liu, Jingyu Kuang, Yuxuan Wang, Ting Duan, Lu Min, Chenyu Lu, Tianyi Zhang, Ruifen Chen, Ying Wu, Lingyun Zhu
Summary: This study provides a unique framework for researchers and clinicians to explore and understand the regulated biological functions of RNF8 in cancer. The identification of new targets and the close relationship between RNF8 and neurodegenerative diseases and tumor-infiltrating immune cells highlight the potential for developing targeted therapies against RNF8 in cancer.
Article
Biochemistry & Molecular Biology
Stephanie Tirman, Annabel Quinet, Matthew Wood, Alice Meroni, Emily Cybulla, Jessica Jackson, Silvia Pegoraro, Antoine Simoneau, Lee Zou, Alessandro Vindigni
Summary: By studying the mechanisms involved in maintaining genome stability, it was found that different pathways are responsible for filling single-stranded DNA gaps throughout the cell cycle, with different proteins and enzymes acting at different stages. Additionally, BRCA1 and BRCA2 play important roles in limiting MRE11 activity for gap filling, and simultaneously targeting fork reversal and gap filling enhances chemosensitivity in BRCA-deficient cells.
Review
Microbiology
Gemma Belli, Neus Colomina, Laia Castells-Roca, Neus P. Lorite
Summary: The sliding clamp PCNA plays a crucial role in DNA replication and is involved in DNA damage tolerance and repair mechanisms through translation modifications. The ubiquitination and sumoylation of PCNA have significant effects on the nervous system and fungal pathogens.
Article
Biochemistry & Molecular Biology
Lingyu Qiu, Wenchao Xu, Xiaopeng Lu, Feng Chen, Yongcan Chen, Yuan Tian, Qian Zhu, Xiangyu Liu, Yongqing Wang, Xin-Hai Pei, Xingzhi Xu, Jun Zhang, Wei-Guo Zhu
Summary: HDAC6 regulates DNA damage signaling by controlling the mismatch repair and nucleotide excision repair pathways. It negatively regulates DNA double-strand break (DSB) repair in an enzyme activity-independent manner. HDAC6 interacts with H2A/H2A.X to prevent its interaction with the E3 ligase RNF168, and DSBs lead to the degradation of HDAC6 and the restoration of the interaction between RNF168 and H2A/H2A.X, facilitating the recruitment of DSB repair factors to chromatin and subsequent DNA repair.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Christopher Mellor, Joelle Nassar, Sasa Svikovic, Julian E. Sale
Summary: PRIMPOL plays a crucial role in integrating with the main pathways of damage tolerance, ensuring cell survival and lesion bypass. It is essential for the survival of cells lacking REV1 and PCNA K164-dependent damage bypass, and it maximizes the effectiveness of their interaction by restricting post-replicative gap length.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Lei Han, Tianming Lan, Desheng Li, Haimeng Li, Linhua Deng, Zhiwei Peng, Shaowen He, Yanqiang Zhou, Ruobing Han, Lingling Li, Yaxian Lu, Haorong Lu, Qing Wang, Shangchen Yang, Yixin Zhu, Yunting Huang, Xiaofang Cheng, Jieyao Yu, Yulong Wang, Heting Sun, Hongliang Chai, Huanming Yang, Xun Xu, Michael Lisby, Quan Liu, Karsten Kristiansen, Huan Liu, Zhijun Hou
Summary: This study presents a high-quality genome of Baylisascaris schroederi, identifying expanded gene families related to epidermal chitin synthesis and amino acid metabolism. Unique genes essential for adapting to the giant panda's diet were found, along with resistance-related genes under positive selection in a captive population. The genome also identified potential drug target proteins, providing insights into the early evolution of roundworms and their adaptation to hosts.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Paula Aguilera, Marion Dubarry, Julien Hardy, Michael Lisby, Marie-Noelle Simon, Vincent Geli
Summary: In yeast cells, C-circles bind to the nuclear pore complex (NPC) and the SAGA-TREX2 complex, promoting the formation of type II survivors. Disrupting the SAGA/TREX2 complex and the nuclear diffusion barrier affects telomere recombination.
Article
Biochemistry & Molecular Biology
Lisa Schubert, Ivo A. Hendriks, Emil P. T. Hertz, Wei Wu, Selene Selles-Baiget, Saskia Hoffmann, Keerthana Stine Viswalingam, Irene Gallina, Satyakrishna Pentakota, Bente Benedict, Joachim Johansen, Katja Apelt, Martijn S. Luijsterburg, Simon Rasmussen, Michael Lisby, Ying Liu, Michael L. Nielsen, Niels Mailand, Julien P. Duxin
Summary: This study reveals an essential role of SCAI in ensuring error-free ICL repair upon activation of the FA pathway. SCAI forms a complex with Pol zeta and localizes to ICLs during DNA replication. In the absence of SCAI, HR-mediated ICL repair is defective, resulting in deletions and radial chromosomes.
Article
Plant Sciences
Lingfei Li, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos-Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C. Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong-Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong Li, Sunil Kumar Sahu, Huanming Yang, Ernest Wu, Joel Sharbrough, Michael Lisby, Xin Liu, Xun Xu, Douglas E. Soltis, Yves Van de Peer, Catherine Kidner, Shouzhou Zhang, Huan Liu
Summary: This study investigates the lineage evolution and shade adaptation of Begonia, one of the most species-rich angiosperm genera, using chromosome-scale genome assemblies for four species and additional genomic data. The results reveal a lineage-specific whole-genome duplication event and expansions of gene families related to shade adaptation.
Article
Biotechnology & Applied Microbiology
Sibo Wang, Hongping Liang, Hongli Wang, Linzhou Li, Yan Xu, Yang Liu, Min Liu, Jinpu Wei, Tao Ma, Cheng Le, Jinlong Yang, Chengzhong He, Jie Liu, Jianming Zhao, Yuxian Zhao, Michael Lisby, Sunil Kumar Sahu, Huan Liu
Summary: Through genome analysis, it was found that Dipterocarpaceae underwent a shared whole-genome duplication event, which significantly impacted the increased copy numbers of genes related to fragrant oleoresin biosynthesis, as well as the expansion of gene families associated with wood formation. This study provides valuable genetic resources for further research on fragrant oleoresins, high-quality timber, and conservation biology of Dipterocarpaceae.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, Zhifeng Wang, Yang Liu, Zhaohui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Baoming Qin, Pengcheng Guo, Guangyao Lai, Pura Munoz-Canoves, Patrick H. Maxwell, Jean Paul Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Junhou Hui, Liqun Wang, Ji-Feng Fei, Ou Wang, Xiaofeng Wei, Haorong Lu, Bo Wang, Shiping Liu, Ying Gu, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J. Cornall, Jan Mulder, Mathias Uhlen, Miguel A. Esteban, Yuxiang Li, Longqi Liu, Xun Xu, Jian Wang
Summary: Spatially resolved transcriptomic technologies enable us to study complex biological processes such as mammalian embryogenesis. However, current methods have limitations in resolution, gene capture, and field of view, which hinders their systematic application to large and three-dimensional mid- and late-gestation embryos. In this study, we developed Stereo-seq, a spatially enhanced resolution omics-sequencing method, by combining DNA nanoball-patterned arrays and in situ RNA capture. We used Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas, MOSTA, which provides single cell resolution and high sensitivity for mapping the kinetics and directionality of transcriptional variation during mouse organogenesis. By utilizing this atlas, we investigated the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues like the dorsal midbrain. Our panoramic atlas will facilitate in-depth research into long-standing questions about normal and abnormal mammalian development.
Review
Cell Biology
Yves Pommier, Andre Nussenzweig, Shunichi Takeda, Caroline Austin
Summary: Human topoisomerases are a family of six enzymes that play essential roles in transcription, DNA replication, chromatin remodeling, and genome organization. However, they can also cause genomic damage, leading to neurological diseases and cancer.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Article
Genetics & Heredity
Margaret Keymakh, Jennifer Dau, Jingyi Hu, Bryan Ferlez, Michael Lisby, J. Brooks Crickard
Summary: Homologous recombination is a DNA repair pathway that uses intact donor DNA to repair damaged DNA and maintain chromosome structure. Regulating DNA sequence transfer is crucial for completing homologous recombination and preserving genome integrity. This study dissects the role of the DNA motor protein Rdh54 in the exchange of genetic information during DNA repair and proposes a model for how Rdh54 regulates strand exchange.
Article
Genetics & Heredity
Takeo Narita, Yoshiki Higashijima, Sinan Kilic, Tim Liebner, Jonas Walter, Chunaram Choudhary
Summary: Chromatin features such as histone H2B N-terminus multisite lysine acetylation are used to identify active enhancers and predict their strength. These chromatin features can also discriminate active enhancers from other regulatory elements and determine their target genes. The intensity of H2BNTac can even predict enhancer strength more accurately than current models.
Article
Biochemistry & Molecular Biology
Paul Cachera, Helen Olsson, Hilde Coumou, Mads L. Jensen, Benjamin J. Sanchez, Tomas Strucko, Marcel van den Broek, Jean-Marc Daran, Michael K. Jensen, Nikolaus Sonnenschein, Michael Lisby, Uffe H. Mortensen
Summary: CRI-SPA allows simple and rapid transfer of chromosomal genetic features between different strains of Saccharomyces cerevisiae. It is highly efficient and reproducible, and even allows marker-free transfer of genetic features. The simplicity, speed, and reliability of CRI-SPA make it a versatile tool for studying biological processes at a systems level.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Sunil Kumar Sahu, Min Liu, Yewen Chen, Jinshan Gui, Dongming Fang, Xiaoli Chen, Ting Yang, Chengzhong He, Le Cheng, Jinlong Yang, Durgesh Nandini Sahu, Linzhou Li, Hongli Wang, Weixue Mu, Jinpu Wei, Jie Liu, Yuxian Zhao, Shouzhou Zhang, Michael Lisby, Xin Liu, Xun Xu, Laigeng Li, Sibo Wang, Huan Liu
Summary: Wood is an important and renewable source of energy, but there are still many aspects of its formation that have not been studied. In this study, chromosome-scale genome assemblies of three timber trees were performed, providing valuable genetic resources for comparative genomic analyses and a better understanding of wood properties in non-model woody species.
Review
Biochemistry & Molecular Biology
Henning Ummethum, Jiayi Li, Michael Lisby, Vibe H. Oestergaard
Summary: This article briefly reviews the details of the CIP2A-TopBP1 interaction, explores their roles in maintaining genome integrity and cancer development, as well as the potential of CIP2A as a therapeutic target.
Letter
Respiratory System
Michael D. Kim, Nathalie Baumlin, Andrea Guerrero-Cignarella, Andreas Schmid, Carolina Aguiar, Mohiuddin Mohiuddin, John S. Dennis, Jasjit S. Ahluwalia, Eleanor L. Leavens, Nikki Nollen, Michael Campos, Matthias Salathe
Article
Plant Sciences
Yang Liu, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Shengdan Wu, Yongbo Liu, Yiqing Gong, Xiuyan Feng, Jianchao Ma, Guanxiao Chang, Jinling Huang, Yong Yang, Hongli Wang, Min Liu, Yan Xu, Hongping Liang, Jin Yu, Yuqing Cai, Zhaowu Zhang, Yannan Fan, Weixue Mu, Sunil Kumar Sahu, Shuchun Liu, Xiaoan Lang, Leilei Yang, Na Li, Sadaf Habib, Yongqiong Yang, Anders J. Lindstrom, Pei Liang, Bernard Goffinet, Sumaira Zaman, Jill L. Wegrzyn, Dexiang Li, Jian Liu, Jie Cui, Eva C. Sonnenschein, Xiaobo Wang, Jue Ruan, Jia-Yu Xue, Zhu-Qing Shao, Chi Song, Guangyi Fan, Zhen Li, Liangsheng Zhang, Jianquan Liu, Zhong-Jian Liu, Yuannian Jiao, Xiao-Quan Wang, Hong Wu, Ertao Wang, Michael Lisby, Huanming Yang, Jian Wang, Xin Liu, Xun Xu, Nan Li, Pamela S. Soltis, Yves Van de Peer, Douglas E. Soltis, Xun Gong, Huan Liu, Shouzhou Zhang
Summary: Cycads, as one of the oldest lineages of seed plants, provide insights into the origin of key innovations and early diversification of seed plants. The genome of Cycas panzhihuaensis was studied, revealing evidence of ancient whole-genome duplication and horizontal gene transfer from fungi. Furthermore, a sex determination mechanism controlled by MADS-Box genes was found to be shared by cycads and Ginkgo. This study fills an important knowledge gap in genome structure and evolution in seed plants.
