Chemical Modifications in Regulatory Regions of DNA and RNA

项目摘要/摘要 DNA基因组和rna转录组都被化学修饰所打断。 四个碱基，这些修饰可以通过以下方式添加到单个核苷酸 特定的酶或由细胞化学安装的，如氧化应激。本节目 寻求通过开发新的化学物质来了解这些碱基修饰发生在哪里 用于修饰的测序方法以及检查这种修饰的生物学结果 通过对写入、读取和擦除蛋白质的生化研究进行修饰 化学修饰。之前NIH对该计划的支持导致了氧化态的发现 鸟嘌呤核苷酸作为G-四链体基因启动子AS的表观遗传性修饰 以及测序方法来表征基因组中的氧化和碱基修饰 转录组。未来的工作将研究关键的DNA修复蛋白，无嘌呤/脱嘧啶 核酸内切酶-1(APE1)、氧化鸟嘌呤糖基酶1(OGG1)、内切酶VIII样蛋白 1(NEIL1)和Cockayne综合征B(CSB)蛋白通过生物物理方法了解 基因调控机制。对于DNA和RNA，纳米孔测序方法将是 高级，用于检测氧化碱基和两种最常见的碱基修饰 RNA、伪尿苷和N6-甲基腺苷。这些不同寻常的碱基被发现比 在经历氧化或炎症应激和病毒感染的细胞中含量丰富。

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.