Yang Jingcheng, Sun Mo, Ran Zihan, Yang Taehwan, Kundnani Deepali L, Storici Francesca, Xu Penghao
State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai 200438, China.
Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong 511462, China.
Bioinform Adv. 2024 May 8;4(1):vbae063. doi: 10.1093/bioadv/vbae063. eCollection 2024.
Ribonucleoside monophosphates (rNMPs) are the most abundant non-standard nucleotides embedded in genomic DNA. If the presence of rNMP in DNA cannot be controlled, it can lead to genome instability. The actual regulatory functions of rNMPs in DNA remain mainly unknown. Considering the association between rNMP embedment and various diseases and cancer, the phenomenon of rNMP embedment in DNA has become a prominent area of research in recent years.
We introduce the rNMPID database, which is the first database revealing rNMP-embedment characteristics, strand bias, and preferred incorporation patterns in the genomic DNA of samples from bacterial to human cells of different genetic backgrounds. The rNMPID database uses datasets generated by different rNMP-mapping techniques. It provides the researchers with a solid foundation to explore the features of rNMP embedded in the genomic DNA of multiple sources, and their association with cellular functions, and, in future, disease. It also significantly benefits researchers in the fields of genetics and genomics who aim to integrate their studies with the rNMP-embedment data.
rNMPID is freely accessible on the web at https://www.rnmpid.org.
核糖核苷单磷酸（rNMPs）是嵌入基因组DNA中最丰富的非标准核苷酸。如果DNA中rNMP的存在无法得到控制，可能会导致基因组不稳定。rNMPs在DNA中的实际调控功能仍然主要未知。鉴于rNMP嵌入与各种疾病和癌症之间的关联，DNA中rNMP嵌入现象近年来已成为一个突出的研究领域。
我们推出了rNMPID数据库，这是首个揭示不同遗传背景的从细菌到人类细胞样本的基因组DNA中rNMP嵌入特征、链偏好及优先掺入模式的数据库。rNMPID数据库使用了由不同rNMP映射技术生成的数据集。它为研究人员提供了一个坚实的基础，以探索嵌入多种来源基因组DNA中的rNMP的特征，以及它们与细胞功能乃至未来疾病的关联。它也极大地造福了旨在将其研究与rNMP嵌入数据相结合的遗传学和基因组学领域的研究人员。
rNMPID可通过网络在https://www.rnmpid.org上免费获取。
