Review
Biochemistry & Molecular Biology
Anzhela Pavlova, Elena A. Kubareva, Mayya Monakhova, Maria Zvereva, Nina G. Dolinnaya
Summary: DNA G-quadruplexes are crucial components of regulatory systems in cells and impact genome integrity by impeding DNA replication. Recent studies have focused on the role of G4s in genomic instability and DNA repair processes, highlighting the intricate balance between stability and instability in the genome.
Review
Biochemistry & Molecular Biology
Rebecca Linke, Michaela Limmer, Stefan A. Juranek, Annkristin Heine, Katrin Paeschke
Summary: In summary, G-quadruplex DNA structures play important roles in cellular function, but can also induce genome instability leading to tumorigenesis and genetic disorders. By interacting with DNA repair proteins and ligands, G4 structures can block specific DNA repair pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Wei-Ting Chen, Huan-Yi Tseng, Chung-Lin Jiang, Chih-Ying Lee, Peter Chi, Liuh-Yow Chen, Kai-Yin Lo, I-Ching Wang, Fu-Jung Lin
Summary: Elp1 depletion exacerbates genomic instability, resulting in chromosome breakage and genotoxic stress-induced DNA fragmentation upon exposure to ionizing radiation (IR). Elp1-deficient cells are sensitive to DNA damage, exhibit impaired cell proliferation, and have defective HR repair. Elp1 regulates RAD51 expression by promoting its translation in response to DNA damage.
JOURNAL OF BIOMEDICAL SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Sunwoo Min, Jae-Hoon Ji, Yungyeong Heo, Hyeseong Cho
Summary: This article discusses how chromosome regulators coordinate DNA repair at active genes. Researchers have found that DNA double-strand breaks prompt a series of genome-organizing proteins to temporarily shut down the transcription of genes into RNA, and then assist in repairing the broken DNA to restore genomic integrity. A better understanding of the importance of regulating chromosome structure could lead to new therapeutic strategies for diseases such as cancer.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Article
Plant Sciences
Jovanka Vladejic, Fen Yang, Eva Dvorak Tomastikova, Jaroslav Dolezel, Jan J. Palecek, Ales Pecinka
Summary: Plants have a sophisticated molecular network to maintain the integrity of genetic information and repair damaged DNA. This study identified and analyzed four uncharacterized Arabidopsis BCP proteins, with BCP1 being the most interesting candidate due to its sensitivity to DNA damage. It was found that BCP1 is regulated by SOG1 and is involved in homology-based repair.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Justyna Antoniuk-Majchrzak, Tuguldur Enkhbaatar, Anna Dlugajczyk, Joanna Kaminska, Marek Skoneczny, Daniel J. Klionsky, Adrianna Skoneczna
Summary: DNA double-strand breaks are harmful to cells, especially when there is no error-free repair pathway available. In this case, error-prone recombination pathways are used to repair the damage, leading to decreased cell viability due to genome rearrangements. Rad51 recombinase is a major protein involved in recombinational repair of DNA damage, and its level is regulated through the ubiquitin-dependent proteolytic pathway. Rad51 can be modified by both ubiquitin and SUMO, and these modifications affect its ability to form and disassemble DNA repair foci, influencing cell cycle progression and cell viability in genotoxic stress conditions.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Laboni Roy, Ananya Roy, Debopriya Bose, Nilanjan Banerjee, Subhrangsu Chatterjee
Summary: A 25 nt G-rich sequence in the promoter region of SMO oncogene was identified to form a parallel G quadruplex (SMO1-GQ). SMO1-GQ is highly conserved in primates. In-depth studies using spectroscopic and computational analysis revealed a stable interaction between SMO1-GQ and the small molecule BRACO-19. Further experiments showed that SMO1-GQ functions as a scaffold for multiple transcription factors and may serve as a promising target for anti-cancer drug development.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Multidisciplinary Sciences
Yu Jiang, Fei Huang, Lu Chen, Jia-Hui Gu, Yun-Wen Wu, Meng-Yan Jia, Zhen Lin, Yong Zhou, Yan-Chu Li, Chao Yu, Ming-Han Tong, Li Shen, Heng-Yu Fan, Qian-Qian Sha
Summary: The R-loop, a three-strand nucleic acid structure, plays important regulatory roles in the meiosis process, particularly in transcriptional regulation and DNA repair. The study of R-loop in mice revealed its predominant distribution at promoter-related regions, its association with high transcription activity, and its crucial role in fertility and DSB repair. These findings highlight the significance of R-loop in spermatogenesis.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Genetics & Heredity
Bilge Argunhan, Hiroshi Iwasaki, Hideo Tsubouchi
Summary: DNA, as the molecule storing chemical instructions for life, is crucial for life, but it is frequently damaged by both external and internal factors, resulting in severe double-strand breaks (DSB). Homologous recombination (HR) is a universal repair mechanism for DSB, where Rad51 and auxiliary factors play essential roles. It is increasingly evident that many HR factors undergo post-translational modifications that are crucial for their function.
Article
Multidisciplinary Sciences
Amer Ali Abd El-Hafeez, Nina Sun, Anirban Chakraborty, Jason Ear, Suchismita Roy, Pranavi Chamarthi, Navin Rajapakse, Soumita Das, Kathryn E. Luker, Tapas K. Hazra, Gary D. Luker, Pradipta Ghosh
Summary: Upon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of the two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DSBs hinges on GIV/Girdin, a guanine nucleotide-exchange modulator of heterotrimeric Gi alpha center dot beta gamma protein. GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1's BRCT-modules via both phospho-dependent and -independent mechanisms. Using another non-overlapping C-terminal motif GIV binds and activates Gi and enhances the freeGb gamma -> PI-3-kinase -> Akt pathway, which promotes survival and is known to suppress HR, favor NHEJ. Absence of GIV, or loss of either of its C-terminal motifs enhanced cell death upon genotoxic stress. Because GIV selectively binds other BRCT-containing proteins suggests that G-proteins may fine-tune sensing, repair, and survival after diverse types of DNA damage.
Article
Multidisciplinary Sciences
Rizky Mutiara Fatimah, Nikko Adhitama, Yasuhiko Kato, Hajime Watanabe
Summary: In this study, a transgenic D. magna line was developed and a reporter gene system expressing mCherry and eGFP was established using CRISPR/Cas technology to evaluate homology-directed repair (HDR). This system can expand our understanding of HDR mechanisms and improve the HDR-based gene-editing system in this species.
SCIENTIFIC REPORTS
(2022)
Review
Plant Sciences
William Agbemafle, Min May Wong, Diane C. Bassham
Summary: This review summarizes key regulatory mechanisms for modulating autophagy through post-translational modification or transcriptional regulation. Plants activate cellular responses to adapt to changing environmental conditions, one of which is autophagy, where cellular components are delivered to the vacuole for degradation. Autophagy is activated by various conditions, and the pathways controlling its activation are being elucidated. However, there is still much to discover regarding how these factors work together to properly modulate autophagy in response to specific signals.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Kangkang Niu, Xiaojuan Zhang, Qisheng Song, Qili Feng
Summary: This study demonstrates that RBM4 promotes mRNA translation of the VEGFA gene by binding to the G4 structure in the IRES.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Xing-Xing Tang, Xue-Ping Wen, Lei Qi, Yang Sui, Ying-Xuan Zhu, Dao-Qiong Zheng
Summary: Chromosomal rearrangements, including both unbalanced and balanced events, play a significant role in phenotypic evolution of organisms. The genetic assay and gene editing tools in Saccharomyces cerevisiae have enabled in-depth exploration of the mechanisms underlying chromosomal rearrangements. By developing methods to generate on-demand rearrangements and map breakpoints, researchers can better understand the contributions of chromosomal rearrangements in driving phenotypic evolution in different S. cerevisiae strains. The knowledge gained from studying yeast can be extended to the genomes of higher eukaryotes due to the evolutionary conservation of DNA replication and recombination mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Esin Orhan, Carolina Velazquez, Imene Tabet, Claude Sardet, Charles Theillet
Summary: RAD51 is an essential gene for cell survival, playing a crucial role in DNA repair and elevated expression in cancers. Targeting RAD51 expression or function could have therapeutic value. It functions as a critical effector of HR, forming homopolymetric filaments at DNA breaks. In normal cells, RAD51 expression is low and tightly regulated, but elevated in many cancers, associated with sensitivity to genotoxic treatment.
Article
Biochemistry & Molecular Biology
Anshika Singhal, Gunjan Arora, Richa Virmani, Parijat Kundu, Tanya Khanna, Andaleeb Sajid, Richa Misra, Jayadev Joshi, Vikas Yadav, Sintu Samanta, Neeru Saini, Amit K. Pandey, Sandhya S. Visweswariah, Christian Hentschker, Doerte Becher, Ulf Gerth, Yogendra Singh
JOURNAL OF BIOLOGICAL CHEMISTRY
(2015)
Review
Microbiology
Atul K. Johri, Ralf Oelmueller, Meenakshi Dua, Vikas Yadav, Manoj Kumar, Narendra Tuteja, Ajit Varma, Paola Bonfante, Bengt L. Persson, Robert M. Stroud
FRONTIERS IN MICROBIOLOGY
(2015)
Article
Multidisciplinary Sciences
Pierre-Marie Badin, Isabelle K. Vila, Danesh H. Sopariwala, Vikas Yadav, Sabina Lorca, Katie Louche, Eun Ran Kim, Qingchun Tong, Min Sup Song, Cedric Moro, Vihang A. Narkar
SCIENTIFIC REPORTS
(2016)
Article
Oncology
Raksha R. Bhat, Puja Yadav, Debashish Sahay, Dharmendra K. Bhargava, Chad J. Creighton, Sahar Yazdanfard, Ahmed Al-rawi, Vikas Yadav, Lanfang Qin, Sarmistha Nanda, Vidyalakshmi Sethunath, Xiaoyong Fu, Carmine De Angelis, Vihang A. Narkar, C. Kent Osborne, Rachel Schiff, Meghana V. Trivedi
BREAST CANCER RESEARCH AND TREATMENT
(2018)
Article
Biochemistry & Molecular Biology
Antonios Matsakas, Vikas Yadav, Sabina Lorca, Vihang Narkar
Article
Cell & Tissue Engineering
Vikas Yadav, Lin Sun, Bruce Panilaitis, David L. Kaplan
JOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE
(2015)
Article
Multidisciplinary Sciences
Danesh H. Sopariwala, Vikas Yadav, Pierre-Marie Badin, Neah Likhite, Megha Sheth, Sabina Lorca, Isabelle K. Vila, Eun Ran Kim, Qingchun Tong, Min Sup Song, George G. Rodney, Vihang A. Narkar
SCIENTIFIC REPORTS
(2017)
Article
Cell Biology
Vikas Yadav, Antonios Matsakas, Sabina Lorca, Vihang A. Narkar
Article
Biochemistry & Molecular Biology
Neah Likhite, Vikas Yadav, Eric J. Milliman, Danesh H. Sopariwala, Sabina Lorca, Nithya P. Narayana, Megha Sheth, Erin L. Reineke, Vincent Giguere, Vihang Narkar
MOLECULAR AND CELLULAR BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Pooja Sanduja, Manish Gupta, Vikas Kumar Somani, Vikas Yadav, Meenakshi Dua, Emanuel Hanski, Abhinay Sharma, Rakesh Bhatnagar, Atul Kumar Johri
NATURE COMMUNICATIONS
(2020)
Review
Microbiology
Puja Yadav, Shalini Verma, Richard Bauer, Monika Kumari, Meenakshi Dua, Atul Kumar Johri, Vikas Yadav, Barbara Spellerberg
Review
Microbiology
Puja Yadav, Nayun Kim, Monika Kumari, Shalini Verma, Tarun Kumar Sharma, Vikas Yadav, Amit Kumar
Summary: G4 DNA, with its noncanonical structure, plays crucial roles in transcriptional and translational regulation, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. Research on the biological roles of G4 DNA and G4 RNA in plants and bacterial pathogens is showing conservation and potential applications.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Danesh H. Sopariwala, Neah Likhite, Gungsheng Pei, Fnu Haroon, Lisa Lin, Vikas Yadav, Zhongming Zhao, Vihang A. Narkar
Summary: ERR alpha is induced in skeletal muscle by hindlimb ischemia or hypoxia, and its overexpression can drive a switch in myofiber type and activate gene programs related to angiogenesis in muscle. This leads to increased baseline capillarity and arterioles, as well as improved perfusion recovery in ischemic muscle, suggesting ERR alpha as a potential target for treating PAD/CLI.
Article
Microbiology
Shalini Verma, Monika Kumari, Anurag Pathak, Vikas Yadav, Atul Kumar Johri, Puja Yadav
Summary: This study investigated the biofilm formation capacity, presence of virulence genes, and antibiotic susceptibility patterns of clinical GBS isolates. The results showed that about one third of GBS strains exhibited penicillin resistance and there was a negative association between having a strong biofilm formation phenotype and penicillin susceptibility.