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SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast.

Sehgal A, Lee CY, Espenshade PJ - PLoS Genet. (2007)

Bottom Line: Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival.Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter.We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, Unites States of America.

ABSTRACT
Retrotransposons are mobile genetic elements that proliferate through an RNA intermediate. Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival. Despite information regarding conditions under which elements are upregulated, much remains to be learned about the regulatory mechanisms or factors controlling retrotransposon expression. Here, we report that low oxygen activates the fission yeast Tf2 family of retrotransposons. Sre1, the yeast ortholog of the mammalian membrane-bound transcription factor sterol regulatory element binding protein (SREBP), directly induces the expression and mobilization of Tf2 retrotransposons under low oxygen. Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter. We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

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Endogenous Solo LTRs Function as Oxygen-Dependent Promoters(A) Scheme for generating Tf2–6 solo LTR. Recombination between intra-element LTRs yields solo LTR. Arrowheads denote position of RT-PCR primers.(B) Wild-type and sre1Δ yeast containing Tf2–6 solo LTR were cultured +/− oxygen for 4 h. Transcription downstream of the LTR was quantified by real-time RT-PCR and normalized to values for wild-type cells + oxygen. Error bars denote standard deviation among three real-time RT-PCR replicates.(C) Wild-type yeast were cultured +/− oxygen for 4 h. Transcription of sequences ∼100 bp downstream of 20 different Tf2 solo LTRs was quantified by real-time RT-PCR as described in Materials and Methods. Fold change in transcription after shifting to low oxygen is shown. Error bars denote standard deviation among three real-time RT-PCR replicates.(D) Wild-type yeast were cultured +/− oxygen for 6 h. Upper panel: Northern analysis using SPCC11E10.07c and SPAC2E1P3.02c probes. Arrows indicate Tf2 LTR derived transcript. Lower panel: RT-PCR to detect transcripts originating either in Tf2 LTR (A–C) or the full mRNA transcripts (B–C). Bold arrows denote transcription initiation sites. Arrowheads denote primer positions.
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pgen-0030131-g005: Endogenous Solo LTRs Function as Oxygen-Dependent Promoters(A) Scheme for generating Tf2–6 solo LTR. Recombination between intra-element LTRs yields solo LTR. Arrowheads denote position of RT-PCR primers.(B) Wild-type and sre1Δ yeast containing Tf2–6 solo LTR were cultured +/− oxygen for 4 h. Transcription downstream of the LTR was quantified by real-time RT-PCR and normalized to values for wild-type cells + oxygen. Error bars denote standard deviation among three real-time RT-PCR replicates.(C) Wild-type yeast were cultured +/− oxygen for 4 h. Transcription of sequences ∼100 bp downstream of 20 different Tf2 solo LTRs was quantified by real-time RT-PCR as described in Materials and Methods. Fold change in transcription after shifting to low oxygen is shown. Error bars denote standard deviation among three real-time RT-PCR replicates.(D) Wild-type yeast were cultured +/− oxygen for 6 h. Upper panel: Northern analysis using SPCC11E10.07c and SPAC2E1P3.02c probes. Arrows indicate Tf2 LTR derived transcript. Lower panel: RT-PCR to detect transcripts originating either in Tf2 LTR (A–C) or the full mRNA transcripts (B–C). Bold arrows denote transcription initiation sites. Arrowheads denote primer positions.

Mentions: The presence of 13 Tf2 elements and 35 Tf2 solo LTRs in the S. pombe genome suggests that a small fraction of mobilization events occur at new positions in the genome [30]. Unlike most characterized retrotransposons [38], fission yeast Tf elements preferentially insert upstream (∼100–400 bp) of RNA polymerase II transcribed genes [30,32,33]. Together with our data, this insertion site bias for RNA polymerase II promoters suggested that Sre1 may control low oxygen expression of genes adjacent to solo LTRs. To test this, we took advantage of the fact that solo LTRs can be formed by homologous recombination. We generated a new Tf2 solo LTR from the ura4+-tagged Tf2–6 element by counterselecting for expression of ura4+ on medium containing 5-fluoroorotic acid (Figure 5A) [39]. Next, we tested the ability of Tf2–6 solo LTR to promote transcription of adjacent sequences using quantitative RT-PCR and primers adjacent to the LTR. We detected Sre1-dependent, oxygen-dependent transcription downstream of Tf2–6 solo LTR, demonstrating that solo LTRs can direct transcription of non-Tf2 sequences (Figure 5B).


SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast.

Sehgal A, Lee CY, Espenshade PJ - PLoS Genet. (2007)

Endogenous Solo LTRs Function as Oxygen-Dependent Promoters(A) Scheme for generating Tf2–6 solo LTR. Recombination between intra-element LTRs yields solo LTR. Arrowheads denote position of RT-PCR primers.(B) Wild-type and sre1Δ yeast containing Tf2–6 solo LTR were cultured +/− oxygen for 4 h. Transcription downstream of the LTR was quantified by real-time RT-PCR and normalized to values for wild-type cells + oxygen. Error bars denote standard deviation among three real-time RT-PCR replicates.(C) Wild-type yeast were cultured +/− oxygen for 4 h. Transcription of sequences ∼100 bp downstream of 20 different Tf2 solo LTRs was quantified by real-time RT-PCR as described in Materials and Methods. Fold change in transcription after shifting to low oxygen is shown. Error bars denote standard deviation among three real-time RT-PCR replicates.(D) Wild-type yeast were cultured +/− oxygen for 6 h. Upper panel: Northern analysis using SPCC11E10.07c and SPAC2E1P3.02c probes. Arrows indicate Tf2 LTR derived transcript. Lower panel: RT-PCR to detect transcripts originating either in Tf2 LTR (A–C) or the full mRNA transcripts (B–C). Bold arrows denote transcription initiation sites. Arrowheads denote primer positions.
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Related In: Results  -  Collection

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pgen-0030131-g005: Endogenous Solo LTRs Function as Oxygen-Dependent Promoters(A) Scheme for generating Tf2–6 solo LTR. Recombination between intra-element LTRs yields solo LTR. Arrowheads denote position of RT-PCR primers.(B) Wild-type and sre1Δ yeast containing Tf2–6 solo LTR were cultured +/− oxygen for 4 h. Transcription downstream of the LTR was quantified by real-time RT-PCR and normalized to values for wild-type cells + oxygen. Error bars denote standard deviation among three real-time RT-PCR replicates.(C) Wild-type yeast were cultured +/− oxygen for 4 h. Transcription of sequences ∼100 bp downstream of 20 different Tf2 solo LTRs was quantified by real-time RT-PCR as described in Materials and Methods. Fold change in transcription after shifting to low oxygen is shown. Error bars denote standard deviation among three real-time RT-PCR replicates.(D) Wild-type yeast were cultured +/− oxygen for 6 h. Upper panel: Northern analysis using SPCC11E10.07c and SPAC2E1P3.02c probes. Arrows indicate Tf2 LTR derived transcript. Lower panel: RT-PCR to detect transcripts originating either in Tf2 LTR (A–C) or the full mRNA transcripts (B–C). Bold arrows denote transcription initiation sites. Arrowheads denote primer positions.
Mentions: The presence of 13 Tf2 elements and 35 Tf2 solo LTRs in the S. pombe genome suggests that a small fraction of mobilization events occur at new positions in the genome [30]. Unlike most characterized retrotransposons [38], fission yeast Tf elements preferentially insert upstream (∼100–400 bp) of RNA polymerase II transcribed genes [30,32,33]. Together with our data, this insertion site bias for RNA polymerase II promoters suggested that Sre1 may control low oxygen expression of genes adjacent to solo LTRs. To test this, we took advantage of the fact that solo LTRs can be formed by homologous recombination. We generated a new Tf2 solo LTR from the ura4+-tagged Tf2–6 element by counterselecting for expression of ura4+ on medium containing 5-fluoroorotic acid (Figure 5A) [39]. Next, we tested the ability of Tf2–6 solo LTR to promote transcription of adjacent sequences using quantitative RT-PCR and primers adjacent to the LTR. We detected Sre1-dependent, oxygen-dependent transcription downstream of Tf2–6 solo LTR, demonstrating that solo LTRs can direct transcription of non-Tf2 sequences (Figure 5B).

Bottom Line: Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival.Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter.We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, Unites States of America.

ABSTRACT
Retrotransposons are mobile genetic elements that proliferate through an RNA intermediate. Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival. Despite information regarding conditions under which elements are upregulated, much remains to be learned about the regulatory mechanisms or factors controlling retrotransposon expression. Here, we report that low oxygen activates the fission yeast Tf2 family of retrotransposons. Sre1, the yeast ortholog of the mammalian membrane-bound transcription factor sterol regulatory element binding protein (SREBP), directly induces the expression and mobilization of Tf2 retrotransposons under low oxygen. Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter. We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

Show MeSH
Related in: MedlinePlus