Article
Chemistry, Multidisciplinary
Yi Zeng, Yujia Mao, Yanjun Chen, Yuhong Wang, Shoujun Xu
Summary: Super-resolution force spectroscopy reveals that single cytosine methylation increases DNA mechanical stability and induces significant chiral selectivity in drug binding. This finding is important for drug design.
CHEMICAL COMMUNICATIONS
(2023)
Review
Cell Biology
James A. Cain, Bertille Montibus, Rebecca J. Oakey
Summary: The mammalian genome is generally lacking in CG dinucleotides, except for CpG islands (CGIs) found in protected regions. CGIs serve as gene regulatory hubs, with a quarter of them located within genes. These intragenic CGIs play a crucial role in gene regulation, influencing transcription activity and transcriptome diversity within genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jizhou Liu, Wei Yang, Xiong Zhang, Yafen Wang, Xiang Zhou
Summary: This method utilizes malononitrile to selectively label 5fC under mild reaction conditions, and then detects and quantifies 5fC through quantitative PCR.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Mansour H. Almatarneh, Ghada G. Kayed, Sanaa S. Al Abbad, Zainab H. A. Alsunaidi, Mohammed S. Al-Sheraideh, Yuming Zhao
Summary: DNA methylation is an important epigenetic mark that regulates gene expression. This study investigated the mechanistic details of the formation of 5-methylcytosine and identified the roles of active site residues and water molecules in the reaction. The results showed that the reaction follows a concerted mechanism involving the participation of water molecules, and alanine and arginine have significant catalytic effects on the process.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Cell Biology
Lee J. Martin, Danya A. Adams, Mark Niedzwiecki, Margaret Wong
Summary: The study showed that epigenetic anomalies in DNA and RNA are prominent in both mouse and human ALS patients, presenting a potential target for disease-modifying therapeutics.
Review
Plant Sciences
Taiko Kim To, Tetsuji Kakutani
Summary: Cytosine is methylated in different ways in plant genomes, and recent studies have uncovered interaction between different methylation patterns. The role of linker histone H1 and variants of histone H2A in DNA methylation dynamics is becoming clearer. These new findings provide further insights into the mechanisms of DNA methylome formation.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Cell Biology
Junnan Liang, Tongtong Liu, Jingyu Liao, Lu Zhang, Mi Zhou, Weiqi Xu, Yi He, Guangzhen Cai, Guannan Jin, Jia Song, Ganxun Li, Huifang Liang, Zeyang Ding, Bixiang Zhang
Summary: The study identified a CIMP-related methylation signature specific for CCA (CMSC) that can classify patients into different risk groups and predict patient outcomes. Additionally, a subset of patients with an unfavorable prognosis correlated with CIMP-H was identified. Gene enrichment analysis suggested a potential mechanism of CIMP as a promoter of carcinogenesis by regulating proliferation.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xu Liu, Emily R. Weikum, Desiree Tilo, Charles Vinson, Eric A. Ortlund
Summary: DNA methylation involves adding a methyl group to a cytosine base, creating new transcription factor binding sites throughout evolution. The glucocorticoid receptor can bind to both unmodified and methylated sequences, with methylation on CpG sites mimicking the interaction with a TpG site. This methyl-specific recognition emerged 420 million years ago and has been conserved during the evolution of the receptor.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Shuxiang Li, Yunhui Peng, David Landsman, Anna R. Panchenko
Summary: This study investigates the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. The results show that methylation induces significant changes in the geometry of DNA, leading to enhanced interactions with the histone octamer and preventing DNA unwrapping.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Jaqueline Loaeza-Loaeza, Berenice Illades-Aguiar, Oscar del Moral-Hernandez, Yaneth Castro-Coronel, Marco A. Leyva-Vazquez, Roberto Dircio-Maldonado, Julio Ortiz-Ortiz, Daniel Hernandez-Sotelo
Summary: This study analyzed the methylation of 8 genes involved in maintaining cell normality and found that high CIMP is significantly associated with the risk of HSIL and CC.
CLINICAL EPIGENETICS
(2022)
Article
Biochemical Research Methods
Daniel M. Sapozhnikov, Moshe Szyf
Summary: This protocol provides an enzyme-free method to achieve targeted DNA demethylation using CRISPR-dCas9, without the involvement of an epigenetic-modifying enzyme. It allows for the evaluation of the functional consequences of DNA demethylation of specific sites and avoids confounding effects of epigenetic enzymes.
Article
Multidisciplinary Sciences
Taiko Kim To, Chikae Yamasaki, Shoko Oda, Sayaka Tominaga, Akie Kobayashi, Yoshiaki Tarutani, Tetsuji Kakutani
Summary: In plant genomes, both mCG and H3K9me2/mCH play important roles in silencing TEs. The establishment of mCH is dependent on the presence of mCG, and the efficiency of mCH targeting depends on the relative levels of mCG in the genome. The study also proposes a model where local positive feedback and global negative feedback regulate DNA methylation patterning.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Pratik Goswami, Martin Bartas, Matej Lexa, Natalia Bohalova, Adriana Volna, Jiri Cerven, Veronika Cervenova, Petr Pecinka, Vladimir Spunda, Miroslav Fojta, Vaclav Brazda
Summary: By analyzing high-frequency mutations of SARS-CoV-2 and their overlay with IR and CpG island loci, this study found that hot-spot mutations of the virus are significantly enriched within these regions. The hypothesis is that hypermethylation of CpG islands may decrease the transcription of viral ORFs and therefore limit the progression of the disease.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Woo Cheol Shim, Sungwook Woo, Joon Won Park
Summary: An atomic force microscopy (AFM)-based quantification method for low-abundance methylated DNA without any treatment to the target DNA is reported. The method employs AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA, showing linear quantification of methylated DNA in the low copy number regime. The potential of this force-mapping-based method for wide applications in early detection of diseases associated with methylated DNA is highlighted.
Article
Genetics & Heredity
Sebastian Kaluscha, Silvia Domcke, Christiane Wirbelauer, Michael B. Stadler, Sevi Durdu, Lukas Burger, Dirk Schuebeler
Summary: Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes by directly inhibiting the binding of transcription factors rather than indirectly inhibiting via recruitment of methyl-CpG-binding domain proteins.
Article
Computer Science, Information Systems
Ritaban Kirtania, Subhashis Banerjee, Sayantan Laha, B. Uma Shankar, Raghunath Chatterjee, Sushmita Mitra
Summary: This study introduced a novel Autoencoder-based strategy for predicting survival of GBM patients, showing superior performance in survival group prediction with high accuracy and AUC values. The biological significance of the extracted genes was analyzed to establish their importance, and the statistical significance of the DeepSGP algorithm's predicted output was confirmed using the concordance index.
Article
Genetics & Heredity
Kaushik Chanda, Sayantan Laha, Raghunath Chatterjee, Debashis Mukhopadhyay
Summary: Aberrant expression of protein-coding genes and microRNAs are implicated in the pathogenesis of Alzheimer's disease (AD). Disrupted miRNA landscape and the involvement of long non-coding RNAs (lncRNA) have been studied in the context of AD. Perturbations in miRNA and lncRNA levels were observed in an AD cell model, with some miRNAs targeting key Receptor Tyrosine Kinase (RTK) known to be implicated in AD.
Article
Biology
Anabik Pal, Akshay Chaturvedi, Aditi Chandra, Raghunath Chatterjee, Swapan Senapati, Alejandro F. Frangi, Utpal Garain
Summary: The study introduces a computational framework to assist human experts in reducing errors in psoriasis diagnosis. By utilizing segmentation and classification methods, neutrophils in skin biopsy images were successfully detected, achieving improved diagnostic performance in experiments.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Virology
Sayantan Laha, Raghunath Chatterjee
Summary: This study analyzed the mutational profile of SARS-CoV-2 in the first year of the pandemic across 35 countries, identifying new mutations and highlighting their potential impact on vaccine efficacy. It emphasizes the importance of actively monitoring country-specific mutations and vaccine effectiveness to combat the spread of the virus.
Article
Biochemistry & Molecular Biology
Joyeeta Chakraborty, Raghunath Chatterjee
Summary: Bacterial virulence factors, including enterotoxins, toxin-antitoxin systems, and collagenase, located in genomic islands of Helicobacter pylori have been found to play important roles in disease progression. These factors can enhance toxin release, worsen ulcers, inhibit immune response, and promote biofilm formation, leading to chronic infection and poor disease prognosis.
BIOSCIENCE REPORTS
(2022)
Article
Biology
Joyeeta Chakraborty, Rudra Prasad Roy, Raghunath Chatterjee, Probal Chaudhuri
Summary: Genomic Islands (GIs) play a crucial role in the evolution and adaptation of prokaryotes. Various GI prediction tools have been developed, but there is a lack of experimentally validated datasets for performance assessment. This study tested the performance of the GI prediction tool Design-Island-II and compared it with other tools. The results showed that Design-Island-II performed the best in terms of sensitivity and F1 score.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Neurosciences
Prosenjit Pal, Shubhrajit Roy, Abhishek Chowdhury, Raghunath Chatterjee, Kunal Ray, Jharna Ray
Summary: Parkinson's disease is a progressive neurodegenerative disorder with a complex etiology. Mutations in the PARK7/DJ-1 gene have been associated with early-onset PD. DJ-1 acts as a putative sensor of oxidative stress, and reduced levels of DJ-1 protein have been observed in the cerebrospinal fluid of PD patients. Our study identified functional involvement of DJ-1 promoter variants and REST-mediated regulation of DJ-1 expression in PD pathogenesis.
NEUROSCIENCE LETTERS
(2023)
Article
Dentistry, Oral Surgery & Medicine
Sayani Mazumder, Baidehi Basu, Jay Gopal Ray, Raghunath Chatterjee
Summary: A study found that the levels of 5 miRNAs in the serum of oral squamous cell carcinoma (OSCC) patients were significantly elevated, with miR-483-5p and miR-31-5p showing potential as early disease markers. These findings suggest that serum miRNAs can be used as non-invasive markers for screening oral cancer and pre-malignant conditions.
ARCHIVES OF ORAL BIOLOGY
(2023)
Article
Dermatology
Torsa Ganguly, Sayantan Laha, Swapan Senapati, Gobinda Chatterjee, Raghunath Chatterjee
Summary: This study investigated the alteration of miRNA levels in the serum of psoriasis patients and found that the changes in miRNA expression were associated with disease severity. This finding may be helpful in monitoring the progression of the disease and determining the therapeutic response.
EXPERIMENTAL DERMATOLOGY
(2023)
Meeting Abstract
Gastroenterology & Hepatology
Sayantani Bhowmik, Sayantan Laha, Suchandrima Ghosh, Swagata Majumdar, Soumyabrata Chatterjee, Simanti Datta, Abhijit Chowdhury, Gopal Krishna Dhali, Raghunath Chatterjee, Soma Banerjee
Article
Biochemistry & Molecular Biology
Dipankar Saha, Prosanto Kr Chowdhury, Amrita Panja, Debashis Pal, Kaustav Nayek, Gispati Chakraborty, Prashant Sharma, Reena Das, Surupa Basu, Raghunath Chatterjee, Anupam Basu
Summary: This study investigated the role of alpha-globin gene deletions in modulating the clinical heterogeneity of beta-thalassemia. The results showed that alpha-globin gene deletions play a role in ameliorating the phenotype in patients with a beta(+)/beta(0) genotype.
Article
Public, Environmental & Occupational Health
Soma Sarkar, Shantanab Das, Kabita Choudhury, Saibal Mukherjee, Raghunath Chatterjee
Summary: The aim of this study is to evaluate the seroprevalence among health care workers (HCWs) pre- and post-vaccination. The study found that almost all HCWs who received two doses of the vaccine developed antibodies, but there was a significant decrease in antibody titre during the 6 to 8 months post-vaccination follow-up, indicating the need for a booster dose. Some vaccinated HCWs with low antibody titre were infected with SARS-CoV-2, but the majority of them only showed mild symptoms and recovered without the need for oxygen support.
EPIDEMIOLOGY AND INFECTION
(2022)
Article
Biochemistry & Molecular Biology
Chinmay Saha, Sayantan Laha, Raghunath Chatterjee, Nitai P. Bhattacharyya
Summary: Altered expression of protein coding genes and long non-coding RNAs have been identified in cells and tissues from COVID-19 patients. Many of these deregulated long non-coding RNAs interact with genes/proteins involved in SARS-CoV-2 infection, modulation by interferon treatment, and identified in CRISPR screening. The deregulated protein coding genes are targets of transcription factors, interferon responsive factors, and other signaling molecules, suggesting joint regulation by long non-coding RNAs and transcription factors in the pathogenesis of COVID-19.
Article
Medicine, General & Internal
Akhilesh Behra, Gobinda Chatterjee, Aditi Chandra, Raghunath Chatterjee
Summary: The HLA-Cw6 allele is significantly associated with psoriasis in Indian population, with positive patients having a more severe form of the disease and scalp involvement. Positive HLA-Cw6 individuals were also found to have a higher Psoriasis Area and Severity Index (PASI) score, indicating a stronger genetic link to the condition's severity.
JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH
(2021)
Article
Multidisciplinary Sciences
Sayantan Laha, Chinmay Saha, Susmita Dutta, Madhurima Basu, Raghunath Chatterjee, Sujoy Ghosh, Nitai P. Bhattacharyya
Summary: Long noncoding RNAs (lncRNAs) show altered expression in SARS-CoV-2 infection, potentially linked to pathways involved in viral infection, inflammation, and immune responses. The dysregulated lncRNAs interact with numerous genes/proteins and microRNAs, and may be regulated by STATs and interferon regulatory factors (IRFs).
