通过iPlex MassARRAY平台构建最小化的表观遗传钟
Ekaterina Davydova1, Alexey Perenkov1, Maria Vedunova1
1Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia.
Genes
|April 27, 2024
概括
这项研究开发了一个最小化的表观遗传时钟,使用来自iPlex MassARRAY技术的向DNA甲基化数据. 时钟显示了作为一个高效的替代品的潜力,以基因组范围的数组为年龄估计.
科学领域:
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 计算生物学 计算生物学
- 老年学是指老年学的学科.
背景情况:
- 表观遗传时钟使用DNA甲基化估计生物和时间年龄.
- 全基因组的方法是全面的,但成本高昂.
- 有针对性的方法为表观遗传时钟的构建提供了效率.
研究的目的:
- 通过使用iPlex MassARRAY技术,评估最小化表观遗传钟的可行性.
- 与既有方法相比,评估年龄预测的准确性.
- 探索用于时钟开发的机器学习模型.
主要方法:
- 在特定基因中的八个CpG位点收集了DNA甲基化数据,使用iPlex MassARRAY和Illumina EPIC阵列.
- 应用机器学习模型 (线性,DNN,GBDT) 包括TabNet.
- 与已建立的表观遗传钟进行时钟性能比较.
主要成果:
- 五个CpG站点显示了显著的年龄相关性和技术之间的良好数据一致性.
- 三个CpG站点的年龄相关性很弱,一致性也很低.
- TabNet模型以5.99.9的平均绝对误差 (MAE) 实现了最佳性能.
- 缩小时钟显示的年龄预测误差略高于现有的时钟.
结论:
- 使用目标甲基化数据最小化的表观遗传钟是可行的.
- iPlex MassARRAY技术可用于针对性的表观遗传时钟构造.
- 这种方法提供了一个潜在的更有效的替代品,以全基因组表观型为年龄估计.
更多相关视频
相关概念视频
Epigenetic Regulation
Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Epigenetic Regulation
Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
Epigenetic Regulation
Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
X-chromosome...
DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Chromatin Modification in iPS Cells
Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...


