Fig. 5.

Model for retrohoming of linear group II intron RNA. RNPs containing linear group II intron RNA recognize DNA target sites and carry out the first step of reverse splicing into the intron insertion site (IS) in the recipient DNA, resulting in ligation of the 3′ end of the intron RNA to the 5′ end of the 3′ exon DNA. The IEP then uses its En domain to cleave the bottom strand between positions +9 and +10 of the 3′ exon (CS) and reverse transcribes the attached linear intron RNA. After resection of the 5′ overhang resulting from the initial staggered double-strand break at the target site, the intron cDNA is linked to the 5′ exon. This attachment step is inaccurate and often occurs with loss of 5′ exon sequences due to excessive resection, insertion of 5′ truncated introns due to incomplete cDNA synthesis or degradation, and/or insertion of extra nucleotide residues at the ligation junction, which is done by a repair DNA polymerase during NHEJ (26–28). As for lariat RNA, retrohoming of the linear intron RNA is likely completed by degradation or displacement of the intron RNA template strand, second-strand DNA synthesis, and sealing of nicks using host enzymes. Intron RNA, red; IEP, gray; recipient DNA, black; cDNA, green; second-strand DNA, blue. 5′SS and 3′SS, 5′ and 3′ splice sites, respectively.