Mapping free-standing homing endonuclease promoters using 5'RLM-RACE

5'RLM-RACE is a PCR-based technique used to map the 5' termini of transcripts in both eukaryotic and prokaryotic organisms. Free-standing homing endonuclease promoters often lack recognizable promoters making predicting the transcriptional start site challenging. Furthermore, homing endonucleases are often expressed at very low levels making transcript mapping a challenge. Here, I present a 5'RLM-RACE protocol with special considerations for the expected abundance of homing endonucleases and for their potential to be subjected to RNA processing events.