Many different cellular pathways have evolved to protect the genome from the 
deleterious effects of DNA damage that result from exposure to chemical and 
physical agents. Among these is a process called transcription-coupled repair 
(TCR) that catalyzes the removal of DNA lesions from the transcribed strand of 
expressed genes, often resulting in a preferential bias of damage clearance from 
this strand relative to its non-transcribed counterpart. Lesions subject to this 
type of repair include cyclobutane pyrimidine dimers that are normally repaired 
by nucleotide excision repair (NER) and thymine glycols (TGs) that are removed 
primarily by base excision repair (BER). While the mechanism underlying TCR is 
not completely clear, it is known that its facilitation requires proteins used 
by other repair pathways like NER. It is also believed that the signal for TCR 
is the stalled RNA polymerase that results when DNA damage prevents its 
translocation during transcription elongation. While there is a clear role for 
some NER proteins in TCR, the involvement of BER proteins is less clear. To 
explore this further, we studied the removal of 7-methylguanine (7MeG) and 
3-methyladenine (3MeA) from the dihydrofolate reductase (dhfr) gene of murine 
cell lines that vary in their repair phenotypes. 7MeG and 3MeA constitute the 
two principal N-methylpurines formed in DNA following exposure to methylating 
agents. In mammalian cells, alkyladenine DNA alkyladenine glycosylase (Aag) is 
the major enzyme required for the repair of these lesions via BER, and their 
removal from the total genome is quite rapid. There is no observable TCR of 
these lesions in specific genes in DNA repair proficient cells; however, it is 
possible that the rapid repair of these adducts by BER masks any TCR. The repair 
of 3MeA and 7MeG was examined in cells lacking Aag, NER, or both Aag and NER to 
determine if rapid overall repair masks TCR. The results show that both 3MeA and 
7MeG are removed without strand bias from the dhfr gene of BER deficient (Aag 
deficient) and NER deficient murine cell lines. Furthermore, repair of 3MeA in 
this region is highly dependent on Aag, but repair of 7MeG is equally efficient 
in the repair proficient, BER deficient, and NER deficient cell lines. 
Strikingly, in the absence of both BER and NER, neither 7MeG nor 3MeA is 
repaired. These results demonstrate that NER, but not TCR, contributes to the 
repair of 7MeG, and to a lesser extent 3MeA.