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Transgenerational inheritance of diet-induced genome rearrangements in Drosophila.

Aldrich JC, Maggert KA - PLoS Genet. (2015)

Bottom Line: Pursuing the relationship between rDNA expression and stability, we have discovered that increased dietary yeast concentration, emulating periods of dietary excess during life, results in somatic rDNA instability and copy number reduction.Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process.Furthermore, adults fed elevated dietary yeast concentrations produce offspring with fewer rDNA copies demonstrating that these effects also occur in the germline, and are transgenerationally heritable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, College of Science, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
Ribosomal RNA gene (rDNA) copy number variation modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila genome. This discovery, along with the link between rDNA, aging, and disease, high-lights the importance of understanding how natural rDNA copy number variation arises. Pursuing the relationship between rDNA expression and stability, we have discovered that increased dietary yeast concentration, emulating periods of dietary excess during life, results in somatic rDNA instability and copy number reduction. Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process. Furthermore, adults fed elevated dietary yeast concentrations produce offspring with fewer rDNA copies demonstrating that these effects also occur in the germline, and are transgenerationally heritable. This finding explains one source of natural rDNA copy number variation revealing a clear long-term consequence of diet.

No MeSH data available.


Related in: MedlinePlus

rDNA deletions persist through multiple generations.(A) Crossing scheme used to establish long-term rDNA deletion stocks and to isolate Y-rDNA arrays for real-time PCR analysis. Nomenclature is as in Fig 5. (B)Y-rDNA copy number of three independent lines (“Lines” 1–3) established from SY30-fed males. Y-rDNA was isolated and quantified two generations after dietary treatment. Percentages calculated relative to Y-rDNA isolated from F0 males (top line in (A)) prior to treatment. Y-rDNA copy number of an I-CreI induced rDNA deletion (“bb-183”) no fewer than sixty generations after it was established, and subsequently maintained on Standard media. Y-rDNA copy number of a mutation-induced rDNA deletion (“10Bt205”) approximately 25 generations after it was established, and subsequently maintained on Standard media. Percentage calculated relative to the control line from which the deletion stock was generated. DNA was isolated from pools of ten sibling females and error bars represent standard error of the mean of three technical replicates.
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pgen.1005148.g006: rDNA deletions persist through multiple generations.(A) Crossing scheme used to establish long-term rDNA deletion stocks and to isolate Y-rDNA arrays for real-time PCR analysis. Nomenclature is as in Fig 5. (B)Y-rDNA copy number of three independent lines (“Lines” 1–3) established from SY30-fed males. Y-rDNA was isolated and quantified two generations after dietary treatment. Percentages calculated relative to Y-rDNA isolated from F0 males (top line in (A)) prior to treatment. Y-rDNA copy number of an I-CreI induced rDNA deletion (“bb-183”) no fewer than sixty generations after it was established, and subsequently maintained on Standard media. Y-rDNA copy number of a mutation-induced rDNA deletion (“10Bt205”) approximately 25 generations after it was established, and subsequently maintained on Standard media. Percentage calculated relative to the control line from which the deletion stock was generated. DNA was isolated from pools of ten sibling females and error bars represent standard error of the mean of three technical replicates.

Mentions: In order for a population to maintain a steady-state rDNA size, natural loss must be balanced by expansion. In Drosophila, rDNA magnification may serve this purpose, although magnification is not wide-spread and is only observed on some chromosomes under certain conditions [30–32, 75]; the determinative characteristics of chromosomes that exhibit magnification remain unknown. To test for this sort of reversion of diet-induced rDNA loss, we established independent lines from SY30-fed males and kept them on Standard food as with any Drosophila strain (Fig 6A). This allowed us to monitor transgenerational rDNA copy number for reversion or continued instability. We tested pooled males from three such independent lines that had been kept for two generations on Standard food after being raised for one generation and 20 days as adult on SY10 or SY30 and found that lost rDNA remained lost. Data shown in Fig 6B (Lines 1, 2, and 3) show standard error of the mean (S.E.M.) to report the average rDNA copy number of individuals line founded by single males. This observation is consistent with published findings (as well as our anecdotal observations) that while some engineered rDNA deletions lines exhibited moderate (~5%) expansion shortly after production [55], they have been otherwise stable, without selection, over many subsequent generations. Indeed, we tested one such line and found that in relation to the progenitor stock, changes—magnification or continued loss—had not occurred after six years on Standard food, corresponding to no fewer than sixty generations (Fig 6B, bb-183). Loss of rDNA was also achieved by passaging the Y,10B in a mutant heterozygous for Su(var)205, which encodes the Heterochromatin Protein 1 gene product. This mutation has been shown to cause rDNA instability [23] and rDNA loss [57], but when the Y,10B “tempered” by the mutation (10Bt205) was returned to a genetic background wild-type for Su(var)205, and passaged for a year (approximately 25 generations) the rDNA loss was not reverted (Fig 6C). These observations suggest that, just like any other polymorphism, rDNA deletions (naturally-occurring or otherwise) persist over multiple generations and that magnification, in contrast, is relatively rare.


Transgenerational inheritance of diet-induced genome rearrangements in Drosophila.

Aldrich JC, Maggert KA - PLoS Genet. (2015)

rDNA deletions persist through multiple generations.(A) Crossing scheme used to establish long-term rDNA deletion stocks and to isolate Y-rDNA arrays for real-time PCR analysis. Nomenclature is as in Fig 5. (B)Y-rDNA copy number of three independent lines (“Lines” 1–3) established from SY30-fed males. Y-rDNA was isolated and quantified two generations after dietary treatment. Percentages calculated relative to Y-rDNA isolated from F0 males (top line in (A)) prior to treatment. Y-rDNA copy number of an I-CreI induced rDNA deletion (“bb-183”) no fewer than sixty generations after it was established, and subsequently maintained on Standard media. Y-rDNA copy number of a mutation-induced rDNA deletion (“10Bt205”) approximately 25 generations after it was established, and subsequently maintained on Standard media. Percentage calculated relative to the control line from which the deletion stock was generated. DNA was isolated from pools of ten sibling females and error bars represent standard error of the mean of three technical replicates.
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Related In: Results  -  Collection

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pgen.1005148.g006: rDNA deletions persist through multiple generations.(A) Crossing scheme used to establish long-term rDNA deletion stocks and to isolate Y-rDNA arrays for real-time PCR analysis. Nomenclature is as in Fig 5. (B)Y-rDNA copy number of three independent lines (“Lines” 1–3) established from SY30-fed males. Y-rDNA was isolated and quantified two generations after dietary treatment. Percentages calculated relative to Y-rDNA isolated from F0 males (top line in (A)) prior to treatment. Y-rDNA copy number of an I-CreI induced rDNA deletion (“bb-183”) no fewer than sixty generations after it was established, and subsequently maintained on Standard media. Y-rDNA copy number of a mutation-induced rDNA deletion (“10Bt205”) approximately 25 generations after it was established, and subsequently maintained on Standard media. Percentage calculated relative to the control line from which the deletion stock was generated. DNA was isolated from pools of ten sibling females and error bars represent standard error of the mean of three technical replicates.
Mentions: In order for a population to maintain a steady-state rDNA size, natural loss must be balanced by expansion. In Drosophila, rDNA magnification may serve this purpose, although magnification is not wide-spread and is only observed on some chromosomes under certain conditions [30–32, 75]; the determinative characteristics of chromosomes that exhibit magnification remain unknown. To test for this sort of reversion of diet-induced rDNA loss, we established independent lines from SY30-fed males and kept them on Standard food as with any Drosophila strain (Fig 6A). This allowed us to monitor transgenerational rDNA copy number for reversion or continued instability. We tested pooled males from three such independent lines that had been kept for two generations on Standard food after being raised for one generation and 20 days as adult on SY10 or SY30 and found that lost rDNA remained lost. Data shown in Fig 6B (Lines 1, 2, and 3) show standard error of the mean (S.E.M.) to report the average rDNA copy number of individuals line founded by single males. This observation is consistent with published findings (as well as our anecdotal observations) that while some engineered rDNA deletions lines exhibited moderate (~5%) expansion shortly after production [55], they have been otherwise stable, without selection, over many subsequent generations. Indeed, we tested one such line and found that in relation to the progenitor stock, changes—magnification or continued loss—had not occurred after six years on Standard food, corresponding to no fewer than sixty generations (Fig 6B, bb-183). Loss of rDNA was also achieved by passaging the Y,10B in a mutant heterozygous for Su(var)205, which encodes the Heterochromatin Protein 1 gene product. This mutation has been shown to cause rDNA instability [23] and rDNA loss [57], but when the Y,10B “tempered” by the mutation (10Bt205) was returned to a genetic background wild-type for Su(var)205, and passaged for a year (approximately 25 generations) the rDNA loss was not reverted (Fig 6C). These observations suggest that, just like any other polymorphism, rDNA deletions (naturally-occurring or otherwise) persist over multiple generations and that magnification, in contrast, is relatively rare.

Bottom Line: Pursuing the relationship between rDNA expression and stability, we have discovered that increased dietary yeast concentration, emulating periods of dietary excess during life, results in somatic rDNA instability and copy number reduction.Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process.Furthermore, adults fed elevated dietary yeast concentrations produce offspring with fewer rDNA copies demonstrating that these effects also occur in the germline, and are transgenerationally heritable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, College of Science, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
Ribosomal RNA gene (rDNA) copy number variation modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila genome. This discovery, along with the link between rDNA, aging, and disease, high-lights the importance of understanding how natural rDNA copy number variation arises. Pursuing the relationship between rDNA expression and stability, we have discovered that increased dietary yeast concentration, emulating periods of dietary excess during life, results in somatic rDNA instability and copy number reduction. Modulation of Insulin/TOR signaling produces similar results, indicating a role for known nutrient sensing signaling pathways in this process. Furthermore, adults fed elevated dietary yeast concentrations produce offspring with fewer rDNA copies demonstrating that these effects also occur in the germline, and are transgenerationally heritable. This finding explains one source of natural rDNA copy number variation revealing a clear long-term consequence of diet.

No MeSH data available.


Related in: MedlinePlus