A method of enhancing drug therapy of a tri-nucleotide repeat expansion disease in a subject in need thereof, comprising administering to said subject an R-loop regulating compound with a tri-nucleotide repeat expansion drug, wherein the tri-nucleotide repeat expansion drug is an oligonucleotide that is complementary to a nucleic acid encoding SPT4 or SUPT4H, wherein the oligonucleotide is a siRNA, a shRNA, an antisense oligonucleotide, or the drug is 6-chloropurine riboside, wherein the R-loop regulating compound is selected from a topoisomerase inhibitor or an RNase H inhibitor, wherein the gene contains a segment of DNA with CAG or CTG tri-nucleotide repeats that are prone to R-loop formation.