Lactylation: The emerging frontier in post-translational modification
Frontiers in Genetics | Epigenomics and Epigenetics section
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2w ago
Lactate, a metabolic byproduct, has gained recognition as a highly influential signaling molecule. Lactylation, an emerging form of post-translational modification derived from lactate, plays a crucial role in numerous cellular processes such as inflammation, embryonic development, tumor proliferation, and metabolism. However, the precise molecular mechanisms through which lactylation governs these biological functions in both physiological and pathological contexts remain elusive. Hence, it is imperative to provide a comprehensive overview of lactylation in order to elucidate its significance ..read more
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Ehmt2 inactivation in pancreatic epithelial cells shapes the transcriptional landscape and inflammation response of the whole pancreas
Frontiers in Genetics | Epigenomics and Epigenetics section
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1M ago
Introduction: The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs. Recently, we have shown that Ehmt2 inactivation in the mouse pancreas alters growth and immune gene expression networks, antagonizing Kras-mediated pancreatic cancer initiation and promotion. Here, we elucidate the essential role of Ehmt2 in maintaining a transcriptional landscape that protects organs from inflammation.Methods: Comparative RNA-seq studies between normal ..read more
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Comparison of the classifiers based on mRNA, microRNA and lncRNA expression and DNA methylation profiles for the tumor origin detection
Frontiers in Genetics | Epigenomics and Epigenetics section
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1M ago
BackgroundTumor tissue origin detection is of great importance in determining the appropriate course of treatment for cancer patients. Classifiers based on gene expression and DNA methylation profiles have been confirmed to be feasible and reliable to predict the tumor primary. However, few works have been performed to compare the performance of these classifiers based on different profiles.MethodsUsing gene expression and DNA methylation profiles from The Cancer Genome Atlas (TCGA) project, eight machine learning methods were employed for the tumor tissue origin detection. We then evaluated t ..read more
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DNA methylation signatures provide novel diagnostic biomarkers and predict responses of immune therapy for breast cancer
Frontiers in Genetics | Epigenomics and Epigenetics section
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1M ago
Breast cancer (BRCA) is one of the most common malignant tumors affecting women worldwide. DNA methylation modifications can influence oncogenic pathways and provide potential diagnostic and therapeutic targets for precision oncology. In this study, we used non-parametric permutation tests to identify differentially methylated positions (DMPs) between paired tumor and normal BRCA tissue samples from the Cancer Genome Atlas (TCGA) database. Then, we applied non-negative matrix factorization (NMF) to the DMPs to derive eight distinct DNA methylation signatures. Among them, signatures Hyper-S3 an ..read more
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STM-ac4C: a hybrid model for identification of N4-acetylcytidine (ac4C) in human mRNA based on selective kernel convolution, temporal convolutional network, and multi-head self-attention
Frontiers in Genetics | Epigenomics and Epigenetics section
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1M ago
N4-acetylcysteine (ac4C) is a chemical modification in mRNAs that alters the structure and function of mRNA by adding an acetyl group to the N4 position of cytosine. Researchers have shown that ac4C is closely associated with the occurrence and development of various cancers. Therefore, accurate prediction of ac4C modification sites on human mRNA is crucial for revealing its role in diseases and developing new diagnostic and therapeutic strategies. However, existing deep learning models still have limitations in prediction accuracy and generalization ability, which restrict their effectiveness ..read more
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Identification of prognostic risk model based on plasma cell markers in hepatocellular carcinoma through single-cell sequencing analysis
Frontiers in Genetics | Epigenomics and Epigenetics section
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1M ago
Hepatocellular carcinoma (HCC) represents a substantial global health burden. Tumorinfiltrating B lymphocytes (TIL-Bs) contribute to tumor progression and significantly impact the efficacy of tumor therapy. However, the characteristics of TIL-Bs in HCC and their effect on HCC therapy remain elusive. Single-cell RNA sequencing (scRNAseq) was applied to investigate the heterogeneity, cellular differentiation and cell-cell communication of TIL-Bs in HCC. Further, the Cancer Genome Atlas-liver hepatocellular carcinoma (TCGA-LIHC) and liver cancer institutes (LCI) cohorts were applied to construct ..read more
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Histone methylation: at the crossroad between circadian rhythms in transcription and metabolism
Frontiers in Genetics | Epigenomics and Epigenetics section
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2M ago
Circadian rhythms, essential 24-hour cycles guiding biological functions, synchronize organisms with daily environmental changes. These rhythms, which are evolutionarily conserved, govern key processes like feeding, sleep, metabolism, body temperature, and endocrine secretion. The central clock, located in the suprachiasmatic nucleus (SCN), orchestrates a hierarchical network, synchronizing subsidiary peripheral clocks. At the cellular level, circadian expression involves transcription factors and epigenetic remodelers, with environmental signals contributing flexibility. Circadian disruption ..read more
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The functions and mechanisms of RNA modification in prostate: Current status and future perspectives
Frontiers in Genetics | Epigenomics and Epigenetics section
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2M ago
The increasing incidence and mortality of prostate cancer worldwide significantly impact the life span of male patients, emphasizing the urgency of understanding its pathogenic mechanism and associated molecular changes that regulate tumor progression for effective prevention and treatment. RNA modification, an important post-transcriptional regulatory process, profoundly influences tumor cell growth and metabolism, shaping cell fate. Over 170 RNA modification methods are known, with prominent research focusing on N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, 5-methylcytidine, ps ..read more
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Editorial: Epigenetic biomarkers for cancer risk stratification and patient management
Frontiers in Genetics | Epigenomics and Epigenetics section
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2M ago
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Editorial: Application of genomics and epigenetics in disease and syndrome classification
Frontiers in Genetics | Epigenomics and Epigenetics section
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2M ago
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