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. 2011 Dec 20;108(51):20351-6.
doi: 10.1073/pnas.1103665108. Epub 2011 Jul 25.

Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5

Joshua A Baller  1 , Jiquan Gao, Daniel F Voytas
Affiliations

Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5

Joshua A Baller et al. Proc Natl Acad Sci U S A. .

Abstract

Integration sites for many retrotransposons and retroviruses are determined by interactions between retroelement-encoded integrases and specific DNA-bound proteins. The Saccharomyces retrotransposon Ty5 preferentially integrates into heterochromatin because of interactions between Ty5 integrase and the heterochromatin protein silent information regulator 4. We mapped over 14,000 Ty5 insertions onto the S. cerevisiae genome, 76% of which occurred in heterochromatin, which is consistent with the known target site bias of Ty5. Using logistic regression, associations were assessed between Ty5 insertions and various chromosomal features such as genome-wide distributions of nucleosomes and histone modifications. Sites of Ty5 insertion, regardless of whether they occurred in heterochromatin or euchromatin, were strongly associated with DNase hypersensitive, nucleosome-free regions flanking genes. Our data support a model wherein silent information regulator 4 tethers the Ty5 integration machinery to domains of heterochromatin, and then, specific target sites are selected based on DNA access, resulting in a secondary target site bias. For insertions in euchromatin, DNA access is the primary determinant of target site choice. One consequence of the secondary target site bias of Ty5 is that insertions in coding sequences occur infrequently, which may preserve genome integrity.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Distribution of Ty5 insertions on chr 3. The x axis denotes position along the chromosome at 1,000-bp resolution. Black bars indicate the number of unambiguous integrations at a particular site; stacked green bars indicate additional ambiguous integrations. Bars above the x axis indicate data from the haploid strain; bars below the x axis denote data from the diploid strain.
Fig. 2.
Fig. 2.
Associations between Ty5 insertions and chromosomal features. Heat maps showing the area under the curve (AUC) of the receiver operating characteristic (ROC) curve from logistic classifiers trained on single features. Actual values shown are AUC-0.5. As such, zero indicates a model of no predictive power, whereas 0.5 and −0.5 indicate models of perfect predictive power. Positive AUCs signify features associated with case integrations; negative AUCs signify sites associated with control integrations. Heat maps for insertions in euchromatin (on the left) and heterochromatin (on the right) were generated from separate models. Details of the datasets used for various chromosomal features can be found in Table S1.
Fig. 3.
Fig. 3.
Ty5 insertions in heterochromatin. Representative heterochromatic domains are shown for the left subtelomeric region of chr 15 (A), the left subtelomeric region of chr 12 (B), and the right subtelomeric region of chr 3 (C). Verified (red) and uncharacterized (tan) ORFs are depicted. Black and green bars indicate the frequency of unambiguous and ambiguous integration events, respectively. Bars above the x axis indicate integrations in the haploid strain; bars below the x axis are integrations in the diploid. The heat map at the top of the graph displays Sir4 occupancy in red; the color intensity was normalized to the chromosomal regions depicted.
Fig. 4.
Fig. 4.
Ty5 insertions near verified ORFs. The X dimension represents position in and around verified ORFs. To account for ORFs of different lengths, the region within the ORFs was scaled as a percentage of ORF length. Datasets were smoothed and scaled for easy comparison. As a result of scaling, all units are arbitrary, and the integrals of all curves are equal.
Fig. 5.
Fig. 5.
A model describing the primary and secondary target site biases of Ty5. Ty5 IN interacts with Sir4, which localizes the integration complex to heterochromatin. This interaction results in the primary target site bias of Ty5, namely the association of ∼75% of Ty5 insertions with domains of heterochromatin. The secondary target site bias of Ty5 is determined by DNA access. Sites in heterochromatin are chosen for being nucleosome-free and accessible to the integration complex. Access to DNA also dictates the preferred integration sites of Ty5 in euchromatin, resulting in integration primarily in nucleosome-free regions flanking genes.
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