AIMC Topic: 5-Methylcytosine

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Brain-derived 5-hydroxymethylcytosine epigenetic scores are related to Alzheimer's disease pathology and cognitive decline.

Acta neuropathologica
BACKGROUND: Cytosine modifications play critical roles in gene regulation and disease pathogenesis. Elucidating novel epigenetic contributions to Alzheimer's disease (AD) could advance diagnostic, prognostic, and therapeutic strategies. 5-hydroxymeth...

A ternary-code DNA methylome atlas of mouse tissues.

Genome biology
BACKGROUND: DNA cytosine modifications, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key epigenetic regulators with distinct functions. Dissecting the ternary code (C, 5mC, 5hmC) across tissues and cell types remains a cri...

A noninvasive and highly efficient epigenetic predictive model for efficacy of the GOLP regimen in patients with intrahepatic cholangiocarcinoma.

Cancer letters
The GOLP regimen (Gemcitabine, Oxaliplatin, Lenvatinib and anti-PD1 antibody) has been a promising first-line treatment for advanced intrahepatic cholangiocarcinoma (iCCA). A noninvasive tool to predict the response to GOLP regimen is needed for clin...

5-Hydroxymethylcytosine signatures as diagnostic biomarkers for septic cardiomyopathy.

Scientific reports
At present, there are currently no molecular biomarkers for the early diagnosis of sepsis cardiomyopathy (SCM) in clinical practice. This study focuses on an in-depth examination of the DNA hydroxymethylation profiles within plasma extracellular vesi...

Identification of m5C RNA modification-related gene signature for predicting prognosis and immune microenvironment-related characteristics of heart failure.

Hereditas
BACKGROUND: Methylation of RNA is involved in many pathophysiological processes. The roles of N6-methyladenosine (m6A) and N7-methylguanosine (m7G) in heart failure (HF) have been established. However, the impact of 5-methylcytosine (m5C) on HF and i...

Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing.

Communications biology
We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK model 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we cons...

Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites.

Methods (San Diego, Calif.)
5-Methylcytosine (m5C) plays a pivotal role in various RNA metabolic processes, including RNA localization, stability, and translation. Current high-throughput sequencing technologies for m5C site identification are resource-intensive in terms of cos...

A hybrid residue based sequential encoding mechanism with XGBoost improved ensemble model for identifying 5-hydroxymethylcytosine modifications.

Scientific reports
RNA modifications play an important role in actively controlling recently created formation in cellular regulation mechanisms, which link them to gene expression and protein. The RNA modifications have numerous alterations, presenting broad glimpses ...

m5C-Seq: Machine learning-enhanced profiling of RNA 5-methylcytosine modifications.

Computers in biology and medicine
Epigenetic modifications, particularly RNA methylation and histone alterations, play a crucial role in heredity, development, and disease. Among these, RNA 5-methylcytosine (m5C) is the most prevalent RNA modification in mammalian cells, essential fo...