Chemical Modifications in Regulatory Regions of DNA and RNA

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.

Grant Number: 5R35GM145237-04
NIH Institute/Center: NIH
Principal Investigator: Cynthia Burrows