Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
Forensic DNA Division, National Forensic Service, Wonju 26460, Republic of Korea.
Forensic Sci Int Genet. 2018 May;34:134-140. doi: 10.1016/j.fsigen.2018.02.013. Epub 2018 Feb 17.
DNA methylation has important biological roles, such as gene expression regulation, as well as practical applications in forensics, such as in body fluid identification and age estimation. DNA methylation often occurs in the CpG site, and methylation within the CpG islands affects various cellular functions and is related to tissue-specific identification. Several programs have been developed to identify CpG islands; however, the size, location, and number of predicted CpG islands are not identical due to different search algorithms. In addition, they only provide structural information for predicted CpG islands without experimental information, such as primer design. We developed an analysis pipeline package, CpGPNP, to integrate CpG island prediction and primer design. CpGPNP predicts CpG islands more accurately and sensitively than other programs, and designs primers easily based on the predicted CpG island locations. The primer design function included standard, bisulfite, and methylation-specific PCR to identify the methylation of particular CpG sites. In this study, we performed CpG island prediction on all chromosomes and compared CpG island search performance of CpGPNP with other CpG island prediction programs. In addition, we compared the position of primers designed for a specific region within the predicted CpG island using other bisulfite PCR primer programs. The primers designed by CpGPNP were used to experimentally verify the amplification of the target region of markers for body fluid identification and age estimation. CpGPNP is freely available at http://forensicdna.kr/cpgpnp/.
DNA 甲基化具有重要的生物学作用，如基因表达调控，以及在法医学中的实际应用，如在体液鉴定和年龄估计。DNA 甲基化通常发生在 CpG 位点，CpG 岛内部的甲基化会影响各种细胞功能，并与组织特异性鉴定有关。已经开发了几个程序来识别 CpG 岛；然而，由于不同的搜索算法，预测 CpG 岛的大小、位置和数量并不完全相同。此外，它们仅提供预测 CpG 岛的结构信息，而没有实验信息，如引物设计。我们开发了一个分析管道包 CpGPNP，以整合 CpG 岛预测和引物设计。CpGPNP 比其他程序更准确和敏感地预测 CpG 岛，并根据预测的 CpG 岛位置轻松设计引物。引物设计功能包括标准、亚硫酸氢盐和甲基化特异性 PCR，以识别特定 CpG 位点的甲基化。在这项研究中，我们对所有染色体进行了 CpG 岛预测，并比较了 CpGPNP 与其他 CpG 岛预测程序的 CpG 岛搜索性能。此外，我们还比较了使用其他亚硫酸氢盐 PCR 引物程序为预测 CpG 岛内特定区域设计的引物的位置。CpGPNP 设计的引物用于实验验证体液鉴定和年龄估计标志物目标区域的扩增。CpGPNP 可在 http://forensicdna.kr/cpgpnp/ 免费获得。
