R-loop is a type of three-stranded nucleic acid structure that is made up of an 
RNA:DNA hybrid, formed due to failing separation of a nascent RNA molecule with 
transcripting template in transcription or by the re-annealing of RNA molecule 
with one of the two strands in a double stranded DNA molecule, along with the 
single stranded DNA, which is either the non-template strand in the 
transcription bubble or the RNA substituted DNA strand. Formation of R-loops can 
occur when transcription goes through a genomic DNA region having a tract of G 
bases in the non-template strand in the transcription bubble or through a type 
of triplet microsatellite DNA sequences that are known to be associated with 
certain human diseases. The negative supercoiling forces accumulated in the 
transcription bubble, and the misprocessing of RNA precursors, as well as the 
delayed utilizations and transportations of RNA molecules to cytoplasm promote R 
loop formation. Many studies show that cells can manage R loop formation with 
efficiency, and can also process the R-loops already formed in the cell, and by 
which, the bad effects of R-loops on DNA replication, gene mutation and 
homologous recombination can be regulated. In this review, we summarize the 
formation and the impacts of R-loops on DNA replication, mutation rates and the 
frequencies of homologous recombination, and also discusse the possible role of 
the R-loop induced DNA replication in mediating trinucleotide repeat expansions 
as seen with those frequently associated with human neuromuscular degenerative 
diseases.