Article
Biology
Filippo Macchi, Eric Edsinger, Kirsten C. Sadler
Summary: The study reveals that the epigenetic machinery of DNA methylation and histone modification is conserved in cephalopods, with DNA methylation enriching gene bodies of highly expressed genes and not decorating transposable elements. This indicates a potential cooperation between 5-methyl-cytosine and the histone code in regulating tissue-specific gene expression in octopuses.
Article
Immunology
Yingxia Zheng, Zheyi Chen, Bingqian Zhou, Shiyu Chen, Li Han, Ningdai Chen, Yanhui Ma, Guohua Xie, Junyao Yang, Hong Nie, Lisong Shen
Summary: This study found that PRMT5 is important for T cell subset differentiation and antitumor immunity. PRMT5 deficiency promotes CD8(+) T cell differentiation into terminal effector cells and impairs the transition to memory precursor cells. Additionally, PRMT5 deficiency accelerates tumor progression.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zhiming Li, Xinzong Zhang, Shiming Xie, Xingping Liu, Caifeng Fei, Xunbin Huang, Yunge Tang, Li-quan Zhou
Summary: This study reveals the important role of Nuclear receptor binding SET domain protein 2 (Nsd2) in spermatogenesis. The loss of Nsd2 leads to apoptosis and abnormal development of spermatogenic cells, as well as dysregulation of genes and histone modifications. Furthermore, Nsd2 deficiency results in the retention of histones and increased protamine proteins in spermatozoa. These findings uncover the involvement of Nsd2 in chromatin remodeling during spermatogenesis and provide insights into the molecular mechanisms of epigenetic abnormalities affecting male reproductive health.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Plant Sciences
Jun-Li Wang, Dong-Wei Di, Pan Luo, Li Zhang, Xiao-Feng Li, Guang-Qin Guo, Lei Wu
Summary: This review focuses on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis, demonstrating that complex signaling pathways affect gene expression and subsequently protein production.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Cell Biology
Ana Teresa Rajado, Nadia Silva, Filipa Esteves, David Brito, Alexandra Binnie, Ines M. Araujo, Clevio Nobrega, Jose Braganca, Pedro Castelo-Branco
Summary: The World Health Organization predicts a drastic increase in the number of people over 60 years old by 2050, highlighting the urgent need for strategies to promote healthy longevity. This study focuses on the role of epigenetics in extending healthspan and describes how aging affects epigenetic processes. It also discusses the positive impact of nutrition and physical exercise on the aging process from an epigenetic perspective.
Article
Biochemistry & Molecular Biology
Nofar Harpaz, Tamir Mittelman, Olga Beresh, Ofir Griess, Noa Furth, Tomer-Meir Salame, Roni Oren, Liat Fellus-Alyagor, Alon Harmelin, Sanda Alexandrescu, Joana Graca Marques, Mariella G. Filbin, Guy Ron, Efrat Shema
Summary: This study adapted CyTOF to analyze histone modifications in DIPG tumor cells and identified two epigenetically distinct subpopulations. These subpopulations were consistent across different tumor lines, and showed differences in proliferation capacity and expression of stem cell and differentiation markers. The study also demonstrated potential interactions between histone modifications and epigenetic alterations during the cell cycle.
Article
Immunology
Dorota Iwaszkiewicz-Grzes, Magdalena Piotrowska, Mateusz Gliwinski, Zuzanna Urban-Wojciuk, Piotr Trzonkowski
Summary: The study revealed that insulin beta chain peptide 9-23 favored specific Tregs expression, while whole insulin activated both Tregs and Teffs. Tregs SPECB:9-23 showed the highest level of expression in crucial genes and lower methylation levels.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Plant Sciences
Maria Vaquero-Sedas, Miguel A. Vega-Palas
Summary: Telomeric regions in Arabidopsis have a bimodal chromatin structure, with telomeres lacking both euchromatic and heterochromatic marks, followed by heterochromatic subtelomeres. The presence of heterochromatic modifications in subtelomeres may play a significant role in telomere biology.
Article
Virology
Maelle Locatelli, Suzanne Faure-Dupuy
Summary: In this review, the authors summarize the current knowledge of how viruses use epigenetic modifications to counteract host antiviral immune responses and discuss the potential use of epigenetic modulators in combating viral infections and virus-induced diseases.
JOURNAL OF VIROLOGY
(2023)
Article
Oncology
Lei Guo, Yi-Tsang Lee, Yubin Zhou, Yun Huang
Summary: Drug resistance is a major obstacle in cancer treatment, and both genetic and epigenetic factors play a role in this process. Epigenetic reprogramming can lead to transcriptional plasticity in tumor cells, driving their transformation towards a persistent state. Targeting epigenetic reprogramming is a new strategy to prevent drug resistance, and combining epigenetic drugs with existing anticancer regimens can overcome resistance.
SEMINARS IN CANCER BIOLOGY
(2022)
Review
Infectious Diseases
Jibran Sualeh Muhammad, Naveed Ahmed Khan, Sutherland K. Maciver, Ahmad M. Alharbi, Hasan Alfahemi, Ruqaiyyah Siddiqui
Summary: Since the discovery of antibiotics, humans have benefited from decreased morbidity and mortality associated with bacterial infections. However, the misuse of antibiotics has led to the emergence of multi-drug resistant bacterial infections, which is a major health concern. Bacteria exposed to inappropriate levels of antibiotics undergo genetic changes that enable them to survive in the host and become more resistant.
Article
Biochemistry & Molecular Biology
Shui-Yi Tung, Ko-Chao Lee, Kam-Fai Lee, Ya-Ling Yang, Wen-Shih Huang, Li-Ya Lee, Wan-Ping Chen, Chin-Chu Chen, Chih-Chuan Teng, Chien-Heng Shen, Meng-Chiao Hsieh, Cheng-Yi Huang, Jiunn-Ming Sheen, Hsing-Chun Kuo
Summary: Erinacine S, a bioactive compound from Hericium erinaceus, induces apoptosis in gastric cancer cells while inhibiting tumor growth in vivo, involving ROS production, extrinsic apoptosis pathways, cell cycle regulation, and activation of specific molecular pathways.
Article
Biotechnology & Applied Microbiology
Martina Tedesco, Francesca Giannese, Dejan Lazarevic, Valentina Giansanti, Dalia Rosano, Silvia Monzanis, Irene Catalano, Elena Grassi, Eugenia R. Zanella, Oronza A. Botrugno, Leonardo Morelli, Paola Panina Bordignon, Giulio Caravagna, Andrea Bertotti, Gianvito Martino, Luca Aldrighetti, Sebastiano Pasqualato, Livio Trusolino, Davide Cittaro, Giovanni Tonon
Summary: Researchers developed a new single-cell method called scGET-seq to comprehensively study open and closed chromatin and record genomic sequences. They also established Chromatin Velocity, a method to identify trajectories of epigenetic modifications at the single-cell level.
NATURE BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Shiv I. S. Grewal
Summary: Heterochromatin plays a crucial role in gene regulation, genome integrity, and silencing repetitive DNA elements. Histone modifications, specifically H3K9 methylation, are essential for the establishment and propagation of heterochromatin domains. Recent studies have highlighted the importance of modified histones, particularly H3K9me3, for epigenetic inheritance during cell division. This review discusses key experiments that have demonstrated the significance of modified histones in this process.
Article
Biochemistry & Molecular Biology
Kei Fukuda, Takeshi Shimi, Chikako Shimura, Takao Ono, Takehiro Suzuki, Kenta Onoue, Satoko Okayama, Hisashi Miura, Ichiro Hiratani, Kazuho Ikeda, Yasushi Okada, Naoshi Dohmae, Shigenobu Yonemura, Azusa Inoue, Hiroshi Kimura, Yoichi Shinkai
Summary: Heterochromatin, a critical architectural feature of eukaryotic chromosomes, plays crucial roles in cell type-specific gene expression and genome stability. The spatial organization of heterochromatin is poorly understood, and this study investigates the role of H3K9 and H3K27 methylation in heterochromatin organization. The findings demonstrate that the loss of H3K9 methylation leads to the redistribution of H3K27me3 and impaired condensation and spatial organization of heterochromatin in mammalian cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Divya Arora, Yogesh Chawla, Basanti Malakar, Archana Singh, Vinay Kumar Nandicoori
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Preeti Jain, Basanti Malakar, Mehak Zahoor Khan, Savita Lochab, Archana Singh, Vinay Kumar Nandicoori
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Immunology
Shruti Srivastava, Madhu Babu Battu, Mehak Zahoor Khan, Vinay Kumar Nandicoori, Sangita Mukhopadhyay
JOURNAL OF IMMUNOLOGY
(2019)
Article
Biology
Savita Lochab, Yogendra Singh, Sagar Sengupta, Vinay Kumar Nandicoori
Article
Biology
Ashima Bhaskar, Santosh Kumar, Mehak Zahoor Khan, Amit Singh, Ved Prakash Dwivedi, Vinay Kumar Nandicoori
Article
Microbiology
Mehak Zahoor Khan, Vinay Kumar Nandicoori
Summary: PknG has the potential to be a promising drug target for adjunct therapy against latent TB, as its inhibition reduces mycobacterial survival in different models and enhances the bactericidal activity of frontline anti-TB drugs. Deletion of pknG significantly reduces the survival rate of Mtb during treatment.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Immunology
Neha Dubey, Mehak Zahoor Khan, Suresh Kumar, Aditya Sharma, Lahari Das, Asani Bhaduri, Yogendra Singh, Vinay Kumar Nandicoori
Summary: PPiA not only assists in the survival of Mtb but also promotes disease progression by affecting host cell status through interaction with host-related factors.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Biochemistry & Molecular Biology
Meetu Agarwal, Vijay Soni, Suresh Kumar, Biplab Singha, Vinay Kumar Nandicoori
Summary: The study demonstrates that the absence of the C-terminal extension region in Mycobacterium tuberculosis GlmU (GlmU(Mt)) abolishes its ability to complement its function, and orthologs from other bacteria also cannot compensate for its function. Point mutants of GlmU(Mt) can successfully restore its biological function by forming heterotrimers.
BIOCHEMICAL JOURNAL
(2021)
Article
Microbiology
Saba Naz, Shruti Dabral, Sathya Narayanan Nagarajan, Divya Arora, Lakshya Veer Singh, Pradeep Kumar, Yogendra Singh, Dhiraj Kumar, Umesh Varshney, Vinay Kumar Nandicoori
Summary: Deleting a DNA repair pathway in Mycobacterium tuberculosis has been shown to increase bacterial mutation rate under antibiotic stress, improve survival in a guinea pig infection model, and potentially identify new antibiotic targets.
Article
Biochemistry & Molecular Biology
Mehak Zahoor Khan, Biplab Singha, Mohammad Farhan Ali, Khushman Taunk, Srikanth Rapole, Samudrala Gourinath, Vinay Kumar Nandicoori
Summary: The study identified AosR as a crucial transcription factor for Mycobacterium tuberculosis survival in the host by mitigating oxidative and nitrosative stress, and promoting growth in the murine lungs and spleen. AosR interacts with SigH to upregulate CysM-dependent cysteine biosynthesis pathway, which is essential for detoxifying host-derived radicals and enhancing bacterial survival in the intracellular environment.
Article
Microbiology
S. Salini, Sinchana G. Bhat, Saba Naz, Ramanathan Natesh, R. Ajay Kumar, Vinay Kumar Nandicoori, Krishna Kurthkoti
Summary: Applying antibiotics to susceptible bacterial cultures generates persistent bacteria that remain susceptible to antibiotics but can endure them. Recent reports have found that antibiotic persisters of mycobacteria experience oxidative stress and develop resistance. Our study reveals that mycobacterial persisters activate the SOS response and upregulate the error-prone DNA polymerase DnaE2, leading to mutagenesis and rapid evolution of antibiotic resistance.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Biplab Singha, Debashree Behera, Mehak Zahoor Khan, Nitesh Kumar Singh, Divya Tej Sowpati, Balasubramanian Gopal, Vinay Kumar Nandicoori
Summary: Through conditional gene replacement, it was found that the o-A gene in Mtb is essential for the survival of the bacteria, and its depletion leads to severe survival defects. RNA-seq analysis showed that o-A directly or indirectly regulates around 57% of the Mtb transcriptome, including 28% of essential genes. Overexpression of o-B, which has about 64% similarity to o-A, failed to compensate for the absence of o-A, suggesting minimal functional redundancy.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biology
Saba Naz, Kumar Paritosh, Priyadarshini Sanyal, Sidra Khan, Yogendra Singh, Umesh Varshney, Vinay Kumar Nandicoori, Digby F. Warner
Summary: Using genome-wide association analysis, we found a strong association between mutations in DNA repair genes and multidrug resistance in clinical strains of Mycobacterium tuberculosis (Mtb). Knockout and complemented strains in Mycobacterium smegmatis and Mtb were used to evaluate the impact of these mutations on drug resistance evolution. Results showed that variant mutations compromised the functions of MutY and UvrB, contributing to better survival under antibiotic/host stress conditions.
Article
Microbiology
Basanti Malakar, Komal Chauhan, Priyadarshini Sanyal, Saba Naz, Haroon Kalam, R. P. Vivek-Ananth, Lakshya Veer Singh, Areejit Samal, Dhiraj Kumar, Vinay Kumar Nandicoori
Summary: This study discovers the regulation of secretion of the virulence factor CFP10 in Mycobacterium tuberculosis (Mtb) through protein phosphorylation. The protein-protein interaction network analysis reveals a complex relationship between phosphorylation and secretion. The dynamic phosphorylation status of CFP10 influences the secretion of virulence factors and impacts bacterial virulence.
Article
Biochemistry & Molecular Biology
Prabhu S. Yavvari, Siddhi Gupta, Divya Arora, Vinay K. Nandicoori, Aasheesh Srivastava, Avinash Bajaj