Homing Introns

Mobile DNA does not only consist of transposable elements. Homing introns are a strange and relatively rare type of mobile DNA. As their name indicates, homing introns are intervening sequences that are inserted into genes between two exons. Each homing intron is located in one unique position within one particular gene of the cell it inhabits. This target gene can exist in two versions, with or without the homing intron inserted.

Movement of homing introns is very restricted as they can only occupy this one specific site. Mobilization can only happen when a cell contains two copies of the target gene, one with and the other without the homing intron. The homing intron will then insert itself into the target gene that lacks a copy of the intron. In eukaryotes, this situation may occur after mating when chromosomes from two different parental cells come together in the zygote. In bacteria, it may occur when DNA enters a recipient cell via any of a variety of mechanisms (see Ch. 18).

Homing introns encode an endonuclease that is responsible for their movement. The endonuclease cleaves a recognition sequence within the target gene and generates short overhanging ends. This double-stranded break triggers a gene conversion event (see Ch. 14) in which the intact version of the gene is copied and used to repair the break (Fig. 15.27). Thus the homing intron merely encodes an enzyme to cut the DNA and leaves the host cell to repair the damage. Insertion of the homing intron disrupts the recognition sequence. Thus the endonuclease only cuts the target gene if the intron is absent. The recognition sequences of homing introns may be as long as 18-20 bp and are the longest and most specific known for any nuclease. This ensures that the intron inserts only into a single unique site in the genome of each cell.

Homing introns of group I use simple endonucleases as described above. These are found in various bacteria and lower eukaryotes. Homing introns of group II are more complex. They are found in bacteria and the organelles of lower eukaryotes. Group II homing introns are retro-elements that use an RNA intermediate. The protein they encode has both endonuclease and reverse transcriptase activity. As before, the endonuclease makes a double-stranded break in the middle of the recognition sequence. Next, the reverse transcriptase generates a DNA copy of the intron for inserting into the break. For a template, it uses the primary transcript from the copy of the target gene that contains the intron (Fig. 15.28). The free 3'-OH generated by the endonuclease cleavage is used as primer for starting DNA synthesis. Consequently, the DNA copy is made already attached to the edge of the double-stranded break.

homing intron A mobile intron that encodes a protein enabling it to insert itself into a recognition sequence within a target gene


One continuous exon

FIGURE 15.27 Homing Intron Inserts in a Unique Location

A homing intron contains a single gene for an endonuclease. This enzyme cleaves a very specific target site, which is only found in a copy of the target gene not containing the homing intron. This situation only occurs when two copies of the target gene are present in a cell, one with the homing intron and one without. The double-stranded break tricks the host cell into repairing the break by gene conversion, thus duplicating the homing intron.


Cleaves target site




Repair by gene conversion

Exon Intron Exon

Two shorter exons

Intron in one copy of gene Empty copy of same gene

Exon Intron Exon Empty site

Transcription mRNA

FIGURE 15.28 Homing Retro-Intron Inserts via RNA Intermediate

Group II homing introns integrate themselves via reverse transcriptase rather than gene conversion. The homing intron expresses an enzyme with both reverse transcriptase and endonuclease activity. The endonuclease generates a double-stranded break at the specific target site. The reverse transcriptase generates a DNA copy of the intron using the 3'-OH of the double-stranded break as a primer for synthesis and the mRNA of the intron as a template. These two functions are shown separated in the figure for clarity. However, in real life, the dsDNA copy of the intron made by reverse transcriptase is attached to the 3'-end of the double-stranded break while it is being made.


Reverse I transcriptase Endo-nuclease

Dual action protein


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