Chemical Modifications in Regulatory Regions of DNA and RNA

项目总结/摘要 DNA基因组和RNA转录组都被化学修饰所打断 这些修饰可以通过以下方式添加到单个核苷酸上： 特定的酶或细胞化学，如氧化应激安装。这个程序 通过开发新的化学物质， 修饰的测序方法以及检查这种修饰的生物学结果 通过对蛋白质的生物化学研究， 化学修饰以前NIH对该项目的支持导致了氧化的发现。 鸟嘌呤核苷酸作为基因启动子的G-四链体中的表观遗传样修饰 以及表征基因组中的氧化和基因组中的碱基修饰的测序方法。 转录组未来的工作将研究关键的DNA修复蛋白，脱嘌呤/脱嘧啶 内切核酸酶-1（APE 1），氧化鸟嘌呤糖基化酶1（OGG 1），内切核酸酶VIII样蛋白 1（NEIL 1）和Cockayne综合征B（CS B）蛋白的生物物理学方法，以了解 基因调控机制。对于DNA和RNA，纳米孔测序方法将被广泛应用。 先进的检测氧化的基地，以及两个最常见的基地修改， RNA、假尿苷和N6-甲基腺苷。发现这些不寻常的碱基 在经历氧化或炎症应激和病毒感染的细胞中丰富。

Project Summary/Abstract Both the DNA genome and the RNA transcriptome are punctuated with chemical modifications to the four bases, and these modifications can either be added to individual nucleotides by specific enzymes or installed by cellular chemistry, such as oxidative stress. This program seeks to understand where these base modifications occur by developing new chemical methods of sequencing for modifications as well as examining the biological outcomes of such modifications through biochemical studies of the proteins that write, read and erase the chemical modifications. Previous NIH support of this program led to the discovery of oxidized guanine nucleotides as epigenetic-like modifications in G-quadruplexes of gene promoters as well as sequencing methods to characterize oxidation in the genome and base modifications in the transcriptome. Future work will study the key DNA repair proteins, apurinic/apyrimidinic endonuclease-1 (APE1), oxidized guanine glycosylase 1 (OGG1), endonuclease VIII-like protein 1 (NEIL1) and Cockayne syndrome B (CSB) protein by biophysical methods to understand the mechanism of gene regulation. For both DNA and RNA, nanopore sequencing methods will be advanced for detection of oxidized bases as well as the two most common base modifications in RNA, pseudouridine and N6-methyladenosine. These unusual bases are found to be more abundant in cells undergoing oxidative or inflammatory stress and viral infection.