ArticleBiochemical and biophysical research communications2008
Histone methylation marks play important roles in predicting the methylation status of CpG islands.
Article in Biochemical and biophysical research communications, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
29 citing papers in PubMed, 56 citations in OpenAlex.
- DeepMethylation: A deep learning framework for tissue-specific DNA methylation prediction and functional variant annotation.PLoS computational biology · 2026Article
- A New Complexity Layer: DNA Methylation and the Predictive Impact of Epigenetic Tests.International journal of molecular sciences · 2026Review
- DeepPGD: A Deep Learning Model for DNA Methylation Prediction Using Temporal Convolution, BiLSTM, and Attention Mechanism.International journal of molecular sciences · 2024Article
- DNA Methylation Profiles ofBiomedicines · 2024Article
- Predicting locus-specific DNA methylation levels in cancer and paracancer tissues.Epigenomics · 2024Article
- The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle.The Plant journal : for cell and molecular biology · 2022Article
- RYBP regulates Pax6 during in vitro neural differentiation of mouse embryonic stem cells.Scientific reports · 2022Article
- Completing Single-Cell DNA Methylome ProfilesFrontiers in genetics · 2022Article
- Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy.Journal of clinical medicine · 2020Article
- PretiMeth: precise prediction models for DNA methylation based on single methylation mark.BMC genomics · 2020Article
- Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues.Epigenetics · 2020Article
- LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data.BMC genomics · 2019Article
- MRCNN: a deep learning model for regression of genome-wide DNA methylation.BMC genomics · 2019Article
- Prediction of genome-wide DNA methylation in repetitive elements.Nucleic acids research · 2017Article
- Genome-Wide Prediction of DNA Methylation Using DNA Composition and Sequence Complexity in Human.International journal of molecular sciences · 2017Article
- Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis.Bioinformatics (Oxford, England) · 2016Article
- Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential.BMC systems biology · 2015Review
- Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.Nature biotechnology · 2015Article
- Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements.Genome biology · 2015Article
- CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome.BMC medical genomics · 2013Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The methylation status of CpG islands is highly correlated with gene expression. Current methods for computational prediction of DNA methylation only utilize DNA sequence features. In this study, besides 35 DNA sequence features, we added four histone methylation marks to predict the methylation status of CpG islands, and improved the accuracy to 89.94%. Also we applied our model to predict the methylation pattern of all the CpG islands in the human genome, and the results are consistent with the previous reports. Our results imply the important roles of histone methylation marks in affecting the methylation status of CpG islands. H3K4me enriched in the methylation-resistant CpG islands could disrupt the contacts between nucleosomes, unravel chromatin and make DNA sequences accessible. And the established open environment may be a prerequisite for or a consequence of the function implementation of zinc finger proteins that could protect CpG islands from DNA methylation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.