On 2016 Nov 28, GERALD SMITH commented:

Comments on an article by Stahl et al., Genetics (2016)

In their article “Apparent epigenetic meiotic double-strand-break disparity in Saccharomyces cerevisiae: A meta-analysis,” STAHL et al. (2016) reanalyze published data on meiotic gene conversion patterns in S. cerevisiae. They infer that the pattern is subject to epigenetic influence and suggest that further experiments, which they are not able to conduct, should be done to test this idea. Relevant data showing this feature had been previously published in Genetics by the group of JÜRG KOHLI.

In their article “The mating-type-related bias of gene conversion in Schizosaccharomyces pombe” PARVANOV et al. (2008) assayed gene conversion at the ura4A hotspot during meiosis. They mated two pairs of strains that were isogenic except for the coupling relations of the mat and ura4A alleles, which are on separate chromosomes. Conversion was assayed after no mitotic divisions (zygotic meiosis) and after extensive (52 or 70) mitotic divisions (azygotic meiosis). The coupling relation made a highly significant (t-test, p < 0.001) 2-fold difference in zygotic meiosis, as also seen in extensive data in BAUR et al. (2005) but no significant difference in azygotic meiosis (ratios of 1.04 and 1.05 were observed). Thus, the coupling effect disappears during mitotic growth, fully consistent with the coupling effect on meiotic gene conversion pattern being epigenetic. BAUR et al. showed that the homolog entering the zygotic crosses in coupling with the h⁺ mating-type allele converted to wt about twice as frequently as did the homolog in coupling with h^-.

The reduction or abolition of the coupling effect by mutations that remove histone modifying enzymes (the acetyl transferases Gcn5 and Ada2 and the deactetylase Clr6), shown by PARVANOV et al., is also strong evidence that this effect is via chromatin structure (one definition of “epigenetic”).

It seems simplest to consider this epigenetic effect to be differential frequency of DSBs at the ura4A hotspot, depending on the coupling relation with the mating-type locus. Differential DSB frequency on the homologs was proposed by STAHL et al. for the effects on gene conversion patterns at HIS4 of S. cerevisiae reported by them and others. In both cases, however, the effect could be via differential repair of a DSB with the sister (resulting in no visible conversion, i.e., restoration) or with the homolog (potentially producing a convertant, either full or half). PARVANOV et al. discuss this possibility of differential repair, citing the differential binding of Swi5 DNA strand-exchange protein to the silent mat2 – mat3 loci in h^- and h⁺ strains (JIA et al. 2004). But this possibility seems at odds with swi2Δ having no significant effect on the coupling effect, yet Swi2 being required for the differential binding of Swi5. In addition, it is unclear that the differential binding of Swi5 to heterochromatin (mat2 – mat3) extends to euchromatin (i.e., at ura4A). Since ura4A has an exceptionally strong meiotic DSB hotspot associated with this transplacement (GREGAN et al. 2005) and since meiotic DSBs are affected by chromatin structure, it seems likely that the effect is via differential DSB frequency, as BAUR et al. and PARVANOV et al. also discuss.

Regardless of the molecular basis of the coupling effect, its disappearance upon mitotic growth of the diploid and its dependence on chromatin modifications establishes the effect as “epigenetic” by a commonly used definition. At the end of their Discussion, STAHL et al. say, “Of course, the conclusions and surmises of this paper are testable by the execution of properly controlled crosses, studies that we are unable to undertake ourselves.” These surmises had been tested years earlier by BAUR et al. and PARVANOV et al. and found to be true. It is unfortunate that their work was not cited by STAHL et al.

BAUR, M., E. HARTSUIKER, E. LEHMANN, K. LUDIN, P. Munz et al., 2005 The meiotic recombination hot spot ura4A in Schizosaccharomyces pombe. Genetics 169: 551-561.

GREGAN, J., P. K. RABITSCH, B. SAKEM, O. CSUTAK, V. LATYPOV et al., 2005 Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Current Biology 15: 1663-1669.

JIA, S., T. YAMADA and S. I. GREWAL, 2004 Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination. Cell 119: 469-480.

PARVANOV, E., J. KOHLI and K. LUDIN, 2008 The mating-type-related bias of gene conversion in Schizosaccharomyces pombe. Genetics 180: 1859-1868.

STAHL, F. W., M. B. REHAN, H. M. FOSS and R. H. BORTS, 2016 Apparent epigenetic meiotic double-strand-break disparity in Saccharomyces cerevisiae: A meta-analysis. Genetics 204: 129-137.

On 2016 Nov 28, GERALD SMITH commented:

Comments on an article by Stahl et al., Genetics (2016)

In their article “Apparent epigenetic meiotic double-strand-break disparity in Saccharomyces cerevisiae: A meta-analysis,” STAHL et al. (2016) reanalyze published data on meiotic gene conversion patterns in S. cerevisiae. They infer that the pattern is subject to epigenetic influence and suggest that further experiments, which they are not able to conduct, should be done to test this idea. Relevant data showing this feature had been previously published in Genetics by the group of JÜRG KOHLI.

In their article “The mating-type-related bias of gene conversion in Schizosaccharomyces pombe” PARVANOV et al. (2008) assayed gene conversion at the ura4A hotspot during meiosis. They mated two pairs of strains that were isogenic except for the coupling relations of the mat and ura4A alleles, which are on separate chromosomes. Conversion was assayed after no mitotic divisions (zygotic meiosis) and after extensive (52 or 70) mitotic divisions (azygotic meiosis). The coupling relation made a highly significant (t-test, p < 0.001) 2-fold difference in zygotic meiosis, as also seen in extensive data in BAUR et al. (2005) but no significant difference in azygotic meiosis (ratios of 1.04 and 1.05 were observed). Thus, the coupling effect disappears during mitotic growth, fully consistent with the coupling effect on meiotic gene conversion pattern being epigenetic. BAUR et al. showed that the homolog entering the zygotic crosses in coupling with the h⁺ mating-type allele converted to wt about twice as frequently as did the homolog in coupling with h^-.

The reduction or abolition of the coupling effect by mutations that remove histone modifying enzymes (the acetyl transferases Gcn5 and Ada2 and the deactetylase Clr6), shown by PARVANOV et al., is also strong evidence that this effect is via chromatin structure (one definition of “epigenetic”).

It seems simplest to consider this epigenetic effect to be differential frequency of DSBs at the ura4A hotspot, depending on the coupling relation with the mating-type locus. Differential DSB frequency on the homologs was proposed by STAHL et al. for the effects on gene conversion patterns at HIS4 of S. cerevisiae reported by them and others. In both cases, however, the effect could be via differential repair of a DSB with the sister (resulting in no visible conversion, i.e., restoration) or with the homolog (potentially producing a convertant, either full or half). PARVANOV et al. discuss this possibility of differential repair, citing the differential binding of Swi5 DNA strand-exchange protein to the silent mat2 – mat3 loci in h^- and h⁺ strains (JIA et al. 2004). But this possibility seems at odds with swi2Δ having no significant effect on the coupling effect, yet Swi2 being required for the differential binding of Swi5. In addition, it is unclear that the differential binding of Swi5 to heterochromatin (mat2 – mat3) extends to euchromatin (i.e., at ura4A). Since ura4A has an exceptionally strong meiotic DSB hotspot associated with this transplacement (GREGAN et al. 2005) and since meiotic DSBs are affected by chromatin structure, it seems likely that the effect is via differential DSB frequency, as BAUR et al. and PARVANOV et al. also discuss.

Regardless of the molecular basis of the coupling effect, its disappearance upon mitotic growth of the diploid and its dependence on chromatin modifications establishes the effect as “epigenetic” by a commonly used definition. At the end of their Discussion, STAHL et al. say, “Of course, the conclusions and surmises of this paper are testable by the execution of properly controlled crosses, studies that we are unable to undertake ourselves.” These surmises had been tested years earlier by BAUR et al. and PARVANOV et al. and found to be true. It is unfortunate that their work was not cited by STAHL et al.

BAUR, M., E. HARTSUIKER, E. LEHMANN, K. LUDIN, P. Munz et al., 2005 The meiotic recombination hot spot ura4A in Schizosaccharomyces pombe. Genetics 169: 551-561.

GREGAN, J., P. K. RABITSCH, B. SAKEM, O. CSUTAK, V. LATYPOV et al., 2005 Novel genes required for meiotic chromosome segregation are identified by a high-throughput knockout screen in fission yeast. Current Biology 15: 1663-1669.

JIA, S., T. YAMADA and S. I. GREWAL, 2004 Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination. Cell 119: 469-480.

PARVANOV, E., J. KOHLI and K. LUDIN, 2008 The mating-type-related bias of gene conversion in Schizosaccharomyces pombe. Genetics 180: 1859-1868.

STAHL, F. W., M. B. REHAN, H. M. FOSS and R. H. BORTS, 2016 Apparent epigenetic meiotic double-strand-break disparity in Saccharomyces cerevisiae: A meta-analysis. Genetics 204: 129-137.