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Meiotic recombination initiation in and around retrotransposable elements in Saccharomyces cerevisiae.

Sasaki M, Tischfield SE, van Overbeek M, Keeney S - PLoS Genet. (2013)

Bottom Line: When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats.From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence.Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

ABSTRACT
Meiotic recombination is initiated by large numbers of developmentally programmed DNA double-strand breaks (DSBs), ranging from dozens to hundreds per cell depending on the organism. DSBs formed in single-copy sequences provoke recombination between allelic positions on homologous chromosomes, but DSBs can also form in and near repetitive elements such as retrotransposons. When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats. A prior study in budding yeast demonstrated that insertion of a Ty retrotransposon into a DSB hotspot can suppress meiotic break formation, but properties of Ty elements in their most common physiological contexts have not been addressed. Here we compile a comprehensive, high resolution map of all Ty elements in the rapidly and efficiently sporulating S. cerevisiae strain SK1 and examine DSB formation in and near these endogenous retrotransposable elements. SK1 has 30 Tys, all but one distinct from the 50 Tys in S288C, the source strain for the yeast reference genome. From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence. Surprisingly, deletion of two Ty elements weakened adjacent DSB hotspots, revealing that at least some Ty insertions promote rather than suppress nearby DSB formation. Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.

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Identifying Ty insertion sites.(A) SK1-derived sequence reads aligned to the S288C genome. Red arrows connected by dotted lines represent paired ends that align near one another. Blue arrows are orphan reads whose mates are aligned inconsistently, e.g., to different chromosomes. Expected patterns are shown for a region where the SK1 genome matches the reference genome, and regions containing a deletion or insertion. (B) Snapshot of the SGRP browser in a simplified cartoon form, depicting SK1-derived reads mapped near YCLWTy5-1. The color scheme is as in (A), plus light brown arrows for reads whose paired ends were not sequenced. (C, D) Confirmation of Ty insertions in SK1 by PCR at URA3 (C) or the YMR118C-ASI1 intergenic region (D). Smaller bands amplified from SK1 genomic DNA are ex vivo deletion products from LTR-LTR recombination during PCR. (E) SK1 sequence reads mapped to the S288C genome near FCF1. Black bars indicate where SK1 Ty1 or Ty2 were previously mapped [25]. Vertical pink arrow shows the single Ty position mapped in this study. The tandemly duplicated gene pair of HXT6 and HXT7 present in S288C is a single copy in SK1, without the intervening sequence.
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pgen-1003732-g002: Identifying Ty insertion sites.(A) SK1-derived sequence reads aligned to the S288C genome. Red arrows connected by dotted lines represent paired ends that align near one another. Blue arrows are orphan reads whose mates are aligned inconsistently, e.g., to different chromosomes. Expected patterns are shown for a region where the SK1 genome matches the reference genome, and regions containing a deletion or insertion. (B) Snapshot of the SGRP browser in a simplified cartoon form, depicting SK1-derived reads mapped near YCLWTy5-1. The color scheme is as in (A), plus light brown arrows for reads whose paired ends were not sequenced. (C, D) Confirmation of Ty insertions in SK1 by PCR at URA3 (C) or the YMR118C-ASI1 intergenic region (D). Smaller bands amplified from SK1 genomic DNA are ex vivo deletion products from LTR-LTR recombination during PCR. (E) SK1 sequence reads mapped to the S288C genome near FCF1. Black bars indicate where SK1 Ty1 or Ty2 were previously mapped [25]. Vertical pink arrow shows the single Ty position mapped in this study. The tandemly duplicated gene pair of HXT6 and HXT7 present in S288C is a single copy in SK1, without the intervening sequence.

Mentions: First, we asked whether SK1 has Tys that are present in S288C. The SGRP data consist of paired-end sequence reads with an average insert of 4–5 kb. These reads can reveal structural differences between a reference genome and the DNA source if the distance between mapped pairs is substantially larger or shorter than the average, or if orphans are present, where one read maps but its mate fails to map or maps to a different genomic region and/or multiple locations (Figure 2A). From inspection of SGRP read maps, we found only one S288C element that was also present in SK1: YCLWTy5-1 at the left end of Chr III (Figure 1, Figure 2B and Table 1). This is the only full-length Ty5 family member in either strain, although there are Ty5 solo LTRs and LTR fragments in both (data not shown). Ty5-family insertions are found preferentially near telomeres and silent mating type loci [reviewed in 11]. YCLWTy5-1 contains mutations rendering it nonfunctional for transposition [31], so this is an ancient Ty present in the last common ancestor of these strains. The remaining 49 S288C Tys are not present in SK1 (Figures S1A, S1B and data not shown). This manual inspection also identified eight S288C Ty sites for which SK1 has one or more Ty elements nearby, subsequently confirmed by PCR (11 Tys total; Figure S1B, Table 1 and data not shown). These novel Tys are at different positions in SK1 than in S288C and often of a different family or in opposite orientation, thus are independent integration events.


Meiotic recombination initiation in and around retrotransposable elements in Saccharomyces cerevisiae.

Sasaki M, Tischfield SE, van Overbeek M, Keeney S - PLoS Genet. (2013)

Identifying Ty insertion sites.(A) SK1-derived sequence reads aligned to the S288C genome. Red arrows connected by dotted lines represent paired ends that align near one another. Blue arrows are orphan reads whose mates are aligned inconsistently, e.g., to different chromosomes. Expected patterns are shown for a region where the SK1 genome matches the reference genome, and regions containing a deletion or insertion. (B) Snapshot of the SGRP browser in a simplified cartoon form, depicting SK1-derived reads mapped near YCLWTy5-1. The color scheme is as in (A), plus light brown arrows for reads whose paired ends were not sequenced. (C, D) Confirmation of Ty insertions in SK1 by PCR at URA3 (C) or the YMR118C-ASI1 intergenic region (D). Smaller bands amplified from SK1 genomic DNA are ex vivo deletion products from LTR-LTR recombination during PCR. (E) SK1 sequence reads mapped to the S288C genome near FCF1. Black bars indicate where SK1 Ty1 or Ty2 were previously mapped [25]. Vertical pink arrow shows the single Ty position mapped in this study. The tandemly duplicated gene pair of HXT6 and HXT7 present in S288C is a single copy in SK1, without the intervening sequence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3757047&req=5

pgen-1003732-g002: Identifying Ty insertion sites.(A) SK1-derived sequence reads aligned to the S288C genome. Red arrows connected by dotted lines represent paired ends that align near one another. Blue arrows are orphan reads whose mates are aligned inconsistently, e.g., to different chromosomes. Expected patterns are shown for a region where the SK1 genome matches the reference genome, and regions containing a deletion or insertion. (B) Snapshot of the SGRP browser in a simplified cartoon form, depicting SK1-derived reads mapped near YCLWTy5-1. The color scheme is as in (A), plus light brown arrows for reads whose paired ends were not sequenced. (C, D) Confirmation of Ty insertions in SK1 by PCR at URA3 (C) or the YMR118C-ASI1 intergenic region (D). Smaller bands amplified from SK1 genomic DNA are ex vivo deletion products from LTR-LTR recombination during PCR. (E) SK1 sequence reads mapped to the S288C genome near FCF1. Black bars indicate where SK1 Ty1 or Ty2 were previously mapped [25]. Vertical pink arrow shows the single Ty position mapped in this study. The tandemly duplicated gene pair of HXT6 and HXT7 present in S288C is a single copy in SK1, without the intervening sequence.
Mentions: First, we asked whether SK1 has Tys that are present in S288C. The SGRP data consist of paired-end sequence reads with an average insert of 4–5 kb. These reads can reveal structural differences between a reference genome and the DNA source if the distance between mapped pairs is substantially larger or shorter than the average, or if orphans are present, where one read maps but its mate fails to map or maps to a different genomic region and/or multiple locations (Figure 2A). From inspection of SGRP read maps, we found only one S288C element that was also present in SK1: YCLWTy5-1 at the left end of Chr III (Figure 1, Figure 2B and Table 1). This is the only full-length Ty5 family member in either strain, although there are Ty5 solo LTRs and LTR fragments in both (data not shown). Ty5-family insertions are found preferentially near telomeres and silent mating type loci [reviewed in 11]. YCLWTy5-1 contains mutations rendering it nonfunctional for transposition [31], so this is an ancient Ty present in the last common ancestor of these strains. The remaining 49 S288C Tys are not present in SK1 (Figures S1A, S1B and data not shown). This manual inspection also identified eight S288C Ty sites for which SK1 has one or more Ty elements nearby, subsequently confirmed by PCR (11 Tys total; Figure S1B, Table 1 and data not shown). These novel Tys are at different positions in SK1 than in S288C and often of a different family or in opposite orientation, thus are independent integration events.

Bottom Line: When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats.From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence.Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

ABSTRACT
Meiotic recombination is initiated by large numbers of developmentally programmed DNA double-strand breaks (DSBs), ranging from dozens to hundreds per cell depending on the organism. DSBs formed in single-copy sequences provoke recombination between allelic positions on homologous chromosomes, but DSBs can also form in and near repetitive elements such as retrotransposons. When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats. A prior study in budding yeast demonstrated that insertion of a Ty retrotransposon into a DSB hotspot can suppress meiotic break formation, but properties of Ty elements in their most common physiological contexts have not been addressed. Here we compile a comprehensive, high resolution map of all Ty elements in the rapidly and efficiently sporulating S. cerevisiae strain SK1 and examine DSB formation in and near these endogenous retrotransposable elements. SK1 has 30 Tys, all but one distinct from the 50 Tys in S288C, the source strain for the yeast reference genome. From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence. Surprisingly, deletion of two Ty elements weakened adjacent DSB hotspots, revealing that at least some Ty insertions promote rather than suppress nearby DSB formation. Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.

Show MeSH
Related in: MedlinePlus