Transcription-coupled repair (TCR) is a pathway dedicated to the removal of 
damage from the template strands of actively transcribed genes. Although the 
detailed mechanism of TCR is not yet understood, it is believed to be triggered 
when a translocating RNA polymerase is arrested at a lesion or unusual structure 
in the DNA. Conventional assays for TCR require high doses of DNA damage for the 
statistical analysis of repair in the individual strands of DNA sequences 
ranging in size from a few hundred bases to 30kb. The single cell gel 
electrophoresis (Comet) assay allows detection of single- or double-strand 
breaks at a 10-100-fold higher level of resolution. Fluorescence in situ 
hybridization (FISH) combined with the Comet assay (Comet-FISH) affords a 
heightened level of sensitivity for the assessment of repair in defined DNA 
sequences of cells treated with physiologically relevant doses of genotoxins. 
This approach also reveals localized susceptibility to chromosomal breakage in 
cells from individuals with hypersensitivity to radiation or chemotherapy. 
Several groups have reported preferential repair in transcriptionally active 
genes or chromosomal domains using Comet-FISH. The prevailing interpretation of 
the behavior of DNA in the Comet assay assumes that the DNA is arranged in loops 
and matrix-attachment sites; that supercoiled, undamaged loops are contained 
within the nuclear matrix and appear in Comet "heads", and that Comet "tails" 
consist of relaxed DNA loops containing one or more breaks. According to this 
model, localization of FISH probes in Comet heads signifies that loops 
containing the targeted sequences are free of damage. This implies that 
preferential repair as detected by Comet-FISH might encompass large chromosomal 
domains containing both transcribed and non-transcribed sequences. We review the 
existing evidence and discuss the implications in relation to current models for 
the molecular mechanism of TCR.