Transposon integration enhances expression of stress response genes

Abstract

Transposable elements possess specific patterns of integration. The biological impact of these integration profiles is not well understood. Tf1, a long-terminal repeat retrotransposon in Schizosaccharomyces pombe, integrates into promoters with a preference for the promoters of stress response genes. To determine the biological significance of Tf1 integration, we took advantage of saturated maps of insertion activity and studied how integration at hot spots affected the expression of the adjacent genes. Our study revealed that Tf1 integration did not reduce gene expression. Importantly, the insertions activated the expression of 6 of 32 genes tested. We found that Tf1 increased gene expression by inserting enhancer activity. Interestingly, the enhancer activity of Tf1 could be limited by Abp1, a host surveillance factor that sequesters transposon sequences into structures containing histone deacetylases. We found the Tf1 promoter was activated by heat treatment and, remarkably, only genes that themselves were induced by heat could be activated by Tf1 integration, suggesting a synergy of Tf1 enhancer sequence with the stress response elements of target promoters. We propose that the integration preference of Tf1 for the promoters of stress response genes and the ability of Tf1 to enhance the expression of these genes co-evolved to promote the survival of cells under stress.

Figure 1.

Tf1 transcription is induced by environmental stress. (A) The Tf1-neo of insertion #5 occurred in Chr #1 between divergent genes ssa1 and upf3. The LTRs are indicated by black triangles and the orientation of Tf1 transcription is from right to left. The distance between the insertion site and the ATGs of the adjacent ORFs is shown. The relative change of Tf1 mRNA in response to environmental stresses for 15 and 60 min was measured by qRT-PCR. The amplicon is indicated by the bar under Tf1. The fold change is represented in the histogram. In all RNA measurements here and in all other experiments except in Figure 4, Table 2 and Supplementary Figure S5, the fold change from three independent plasmid transformants is averaged. One standard deviation is represented with error bars. (B) The response of Tf1 expression to heat (15 and 60 min) in each of the 14 insertion strains was measured by qRT-PCR and is shown in histograms. (C) qRT-PCR was used to measure the response of Tf1 expression to oxidative stress in a representative group of the insertion strains. The inductions of Tf1 mRNAs after 15 and 60 min of treatment are shown.

Figure 2.

Tf1 insertion increased the expression of ssa1. (A) The levels of ssa1 mRNA from cells lacking Tf1 and from cells with Tf1 upstream of ssa1 was measured on RNA blots. The amount of ssa1 mRNA relative to actin mRNA is shown in the histogram. (B) The transcription start site of ssa1 mRNA from cells with and without the Tf1 insertion at ssa1 was mapped by 5′ RACE and sequencing of the products. (C) The levels of ssa1 mRNA from cells without Tf1 and from all the 14 strains with Tf1 insertions were measured on an RNA blot. The histogram shows for each insertion strain the change in the expression of ssa1 mRNA caused by the insertion of Tf1.

Figure 3.

Tf1 insertion increased the expression of spn7 and css1 when cells were exposed to stress. (A and B) The increase in spn7 mRNA caused by Tf1 insertion upstream of spn7 was measured on RNA blots. Cells were heat treated for 0, 15 and 60 min or (B) treated with peroxide for 0, 15 and 60 min. (C and D) The increase in css1 mRNA caused by Tf1 insertion upstream of css1 was measured on RNA blots. The cells were either treated with (C) heat or (D) hydrogen peroxide. (E and F) The transcription start site of (E) spn7 mRNA or (F) css1 mRNA in cells with or without upstream insertions of Tf1 was mapped by 5′ RACE followed by sequencing of the products. The cells were treated with heat and peroxide.

Figure 4.

Abp1 restricted the enhancer activity of Tf1 and limited the expression of adjacent genes. (A) The effect of the Tf1 insertion on levels of css1 mRNA in cells with and without abp1 was measured on RNA blots. The strains analyzed lacked Tf1 or contained a Tf1 insertion upstream of css1. RNA from cells lacking abp1 was analyzed revealing that Abp1 restricted the activation of css1. The levels of css1 mRNA relative to actin mRNA were averaged from three independent strains in the histogram. (B) The effect of Tf1 integration on the expression of SPBC4F6.05c was analyzed as described in (A). The transcription start sites for (C) css1 and (D) SPBC4F6.05c were determined by 5′ RACE followed by sequencing of the products.

Figure 5.

Upf1 restricted the increased expression of SPNCRNA.623 by the enhancer activity of Tf1. (A) The orientation and position of the Tf1 insertion between SPNCRNA.623 and SPAC24B11.09 is shown. The sequence of the probe is represented by a line underneath SPNCRNA.623. The distances from the Tf1 insertion to the adjacent ORFs is shown above the line. (B) The levels of SPNCRNA.623 RNA were measured from strains that lacked Tf1 or contained Tf1 inserted downstream of SPNCRNA.623. The RNA blots were hybridized with strand-specific probes to determine the orientation of SPNCRNA.623 transcription. In addition, RNA from cells lacking upf1 was analyzed to determine whether NMD limited the enhanced expression of SPNCRNA.623 by Tf1. The levels of SPNCRNA.623 RNA are shown in the histogram. (C) The 5′ and 3′ termini of SPNCRNA.623 RNA were determined by RACE followed by sequencing. The distance from the 5′ and 3′ termini of SPNCRNA.623 to the adjacent ORFs is shown above the line. The termini are represented by the arrows labeled a and b.