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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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Related in: MedlinePlus

Systematic Ty mapping.(A) Mapping strategy. (B) Ty in the PEX25-CAR1 intergenic region. (C) Number of SGRP reads supporting each Ty position in SK1. The observed distribution of read frequencies around each of 28 Ty sites is compared to that expected from a Poisson distribution with the same mean (λ = 8.6). (D) Copy number of Tys from different families in SK1 and S288C.
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pgen-1003732-g003: Systematic Ty mapping.(A) Mapping strategy. (B) Ty in the PEX25-CAR1 intergenic region. (C) Number of SGRP reads supporting each Ty position in SK1. The observed distribution of read frequencies around each of 28 Ty sites is compared to that expected from a Poisson distribution with the same mean (λ = 8.6). (D) Copy number of Tys from different families in SK1 and S288C.

Mentions: Third, we used an unbiased approach to ensure that all Ty elements were identified, using SGRP data and a paired-end genomic sequence library from NKY291, a Kleckner-lineage haploid. We retrieved sequence pairs in which one mate matched non-LTR parts of Tys, then mapped the non-Ty mate on the S288C genome (277 SGRP reads and 4,963 NYK291 reads, <1% of the total from each). Tys appear as clusters of reads pointing from both directions at the insertion site (Figures 3A and 3B). We identified all of the Tys described above, and also found an additional element on Chr II, present in both libraries and confirmed by PCR (data not shown). On average, 8.6 SGRP reads tagged each SK1-specific Ty or cluster of Tys, and the read counts matched a Poisson distribution (Figure 3C). Thus, we estimate the probability to be <0.0002 that a Ty was missed because of chance failure to recover supporting reads. The NKY291 library provided even more reads identifying each Ty (mean 158.2, range 30–304), so it is highly likely we identified all of the Tys in SK1.


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

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

Systematic Ty mapping.(A) Mapping strategy. (B) Ty in the PEX25-CAR1 intergenic region. (C) Number of SGRP reads supporting each Ty position in SK1. The observed distribution of read frequencies around each of 28 Ty sites is compared to that expected from a Poisson distribution with the same mean (λ = 8.6). (D) Copy number of Tys from different families in SK1 and S288C.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003732-g003: Systematic Ty mapping.(A) Mapping strategy. (B) Ty in the PEX25-CAR1 intergenic region. (C) Number of SGRP reads supporting each Ty position in SK1. The observed distribution of read frequencies around each of 28 Ty sites is compared to that expected from a Poisson distribution with the same mean (λ = 8.6). (D) Copy number of Tys from different families in SK1 and S288C.
Mentions: Third, we used an unbiased approach to ensure that all Ty elements were identified, using SGRP data and a paired-end genomic sequence library from NKY291, a Kleckner-lineage haploid. We retrieved sequence pairs in which one mate matched non-LTR parts of Tys, then mapped the non-Ty mate on the S288C genome (277 SGRP reads and 4,963 NYK291 reads, <1% of the total from each). Tys appear as clusters of reads pointing from both directions at the insertion site (Figures 3A and 3B). We identified all of the Tys described above, and also found an additional element on Chr II, present in both libraries and confirmed by PCR (data not shown). On average, 8.6 SGRP reads tagged each SK1-specific Ty or cluster of Tys, and the read counts matched a Poisson distribution (Figure 3C). Thus, we estimate the probability to be <0.0002 that a Ty was missed because of chance failure to recover supporting reads. The NKY291 library provided even more reads identifying each Ty (mean 158.2, range 30–304), so it is highly likely we identified all of the Tys in SK1.

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