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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

Larval diet influences rDNA activity and stability.(A) Real time PCR quantification of cDNAs derived from unprocessed (ETS-18S junction) pre-rRNA from larvae fed either SY10 or SY30 diets. Values were normalized to the genomic DNA copies of tRNAK-CTT genes and proportions plotted relative to Standard-fed larvae (defined as 100%). Error bars report standard deviation of RNA quantities derived from five independent pools of larvae for each condition, and indicate differences between populations exposed to altered dietary source. Although population distributions (shown) overlap, average rRNA expressions of SY10 vs SY30 differ. (B) Gallery of representative salivary gland nuclei obtained from SY10-fed larvae. Frequency of nuclei with multiple nucleoli was 7% ± 6% (S.D.), N = 337. α-Fibrillarin stains nucleoli red, DAPI stains DNA blue. (C) Gallery of representative salivary gland nuclei obtained from SY30-fed larvae, stained as in (B). Frequency of nuclei with multiple nucleoli was 40% ± 24% (S.D.), N = 522. (D) Real-time quantitative PCR analysis of 35S rDNA copy number in adult males raised on SY10 or SY30 as larvae. Percentages calculated relative to isogenic flies raised on standard food (defined as 100%). Error bars are standard deviation of three independent biological replicates and 3–4 technical replicates of each, and so contain pooled standard deviations of the populations and standard errors of the quantification. (E) Quantification of acidified-alcohol-extractable pigment from whitemottled-4 flies raised on SY10 and SY30. Error bars are standard deviation of three parallel biological replicates each containing heads from 20 individuals. All P-values (in (A), (D), and (E)) were calculated using Student’s t-test.
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pgen.1005148.g001: Larval diet influences rDNA activity and stability.(A) Real time PCR quantification of cDNAs derived from unprocessed (ETS-18S junction) pre-rRNA from larvae fed either SY10 or SY30 diets. Values were normalized to the genomic DNA copies of tRNAK-CTT genes and proportions plotted relative to Standard-fed larvae (defined as 100%). Error bars report standard deviation of RNA quantities derived from five independent pools of larvae for each condition, and indicate differences between populations exposed to altered dietary source. Although population distributions (shown) overlap, average rRNA expressions of SY10 vs SY30 differ. (B) Gallery of representative salivary gland nuclei obtained from SY10-fed larvae. Frequency of nuclei with multiple nucleoli was 7% ± 6% (S.D.), N = 337. α-Fibrillarin stains nucleoli red, DAPI stains DNA blue. (C) Gallery of representative salivary gland nuclei obtained from SY30-fed larvae, stained as in (B). Frequency of nuclei with multiple nucleoli was 40% ± 24% (S.D.), N = 522. (D) Real-time quantitative PCR analysis of 35S rDNA copy number in adult males raised on SY10 or SY30 as larvae. Percentages calculated relative to isogenic flies raised on standard food (defined as 100%). Error bars are standard deviation of three independent biological replicates and 3–4 technical replicates of each, and so contain pooled standard deviations of the populations and standard errors of the quantification. (E) Quantification of acidified-alcohol-extractable pigment from whitemottled-4 flies raised on SY10 and SY30. Error bars are standard deviation of three parallel biological replicates each containing heads from 20 individuals. All P-values (in (A), (D), and (E)) were calculated using Student’s t-test.

Mentions: We fist confirmed that altered diet affected rRNA expression. We could discriminate accumulated mature rRNA products (18S, 28S, 5.8S), for instance bound in ribosomes, from actively-transcribed pre-rRNAs (35S, or 45S in some organisms) by detecting the quantity of cDNA derived from the pre-processed 5’-most sequence of the 35S primary transcript containing the External Transcribed Spacer (ETS). The ETS is constitutively processed during maturation of the pre-rRNA 35S transcript and quickly degraded, and is therefore used to measure de novo rDNA expression [26, 53, 54]. We compared male flies of genotype yellow1white67c23/Dp(1;Y) y+, P{w = RS5}10B (henceforth Y,10B), upon which we have performed other studies of the ribosomal rDNA [24, 41, 55–58]. We detected an approximately 50% increase in pre-rRNA levels in populations of second instar larvae raised on SY30 compared to Standard media (Fig 1A), confirming the suitability of these media for this study.


Transgenerational inheritance of diet-induced genome rearrangements in Drosophila.

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

Larval diet influences rDNA activity and stability.(A) Real time PCR quantification of cDNAs derived from unprocessed (ETS-18S junction) pre-rRNA from larvae fed either SY10 or SY30 diets. Values were normalized to the genomic DNA copies of tRNAK-CTT genes and proportions plotted relative to Standard-fed larvae (defined as 100%). Error bars report standard deviation of RNA quantities derived from five independent pools of larvae for each condition, and indicate differences between populations exposed to altered dietary source. Although population distributions (shown) overlap, average rRNA expressions of SY10 vs SY30 differ. (B) Gallery of representative salivary gland nuclei obtained from SY10-fed larvae. Frequency of nuclei with multiple nucleoli was 7% ± 6% (S.D.), N = 337. α-Fibrillarin stains nucleoli red, DAPI stains DNA blue. (C) Gallery of representative salivary gland nuclei obtained from SY30-fed larvae, stained as in (B). Frequency of nuclei with multiple nucleoli was 40% ± 24% (S.D.), N = 522. (D) Real-time quantitative PCR analysis of 35S rDNA copy number in adult males raised on SY10 or SY30 as larvae. Percentages calculated relative to isogenic flies raised on standard food (defined as 100%). Error bars are standard deviation of three independent biological replicates and 3–4 technical replicates of each, and so contain pooled standard deviations of the populations and standard errors of the quantification. (E) Quantification of acidified-alcohol-extractable pigment from whitemottled-4 flies raised on SY10 and SY30. Error bars are standard deviation of three parallel biological replicates each containing heads from 20 individuals. All P-values (in (A), (D), and (E)) were calculated using Student’s t-test.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4401788&req=5

pgen.1005148.g001: Larval diet influences rDNA activity and stability.(A) Real time PCR quantification of cDNAs derived from unprocessed (ETS-18S junction) pre-rRNA from larvae fed either SY10 or SY30 diets. Values were normalized to the genomic DNA copies of tRNAK-CTT genes and proportions plotted relative to Standard-fed larvae (defined as 100%). Error bars report standard deviation of RNA quantities derived from five independent pools of larvae for each condition, and indicate differences between populations exposed to altered dietary source. Although population distributions (shown) overlap, average rRNA expressions of SY10 vs SY30 differ. (B) Gallery of representative salivary gland nuclei obtained from SY10-fed larvae. Frequency of nuclei with multiple nucleoli was 7% ± 6% (S.D.), N = 337. α-Fibrillarin stains nucleoli red, DAPI stains DNA blue. (C) Gallery of representative salivary gland nuclei obtained from SY30-fed larvae, stained as in (B). Frequency of nuclei with multiple nucleoli was 40% ± 24% (S.D.), N = 522. (D) Real-time quantitative PCR analysis of 35S rDNA copy number in adult males raised on SY10 or SY30 as larvae. Percentages calculated relative to isogenic flies raised on standard food (defined as 100%). Error bars are standard deviation of three independent biological replicates and 3–4 technical replicates of each, and so contain pooled standard deviations of the populations and standard errors of the quantification. (E) Quantification of acidified-alcohol-extractable pigment from whitemottled-4 flies raised on SY10 and SY30. Error bars are standard deviation of three parallel biological replicates each containing heads from 20 individuals. All P-values (in (A), (D), and (E)) were calculated using Student’s t-test.
Mentions: We fist confirmed that altered diet affected rRNA expression. We could discriminate accumulated mature rRNA products (18S, 28S, 5.8S), for instance bound in ribosomes, from actively-transcribed pre-rRNAs (35S, or 45S in some organisms) by detecting the quantity of cDNA derived from the pre-processed 5’-most sequence of the 35S primary transcript containing the External Transcribed Spacer (ETS). The ETS is constitutively processed during maturation of the pre-rRNA 35S transcript and quickly degraded, and is therefore used to measure de novo rDNA expression [26, 53, 54]. We compared male flies of genotype yellow1white67c23/Dp(1;Y) y+, P{w = RS5}10B (henceforth Y,10B), upon which we have performed other studies of the ribosomal rDNA [24, 41, 55–58]. We detected an approximately 50% increase in pre-rRNA levels in populations of second instar larvae raised on SY30 compared to Standard media (Fig 1A), confirming the suitability of these media for this study.

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