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Transvection-based gene regulation in Drosophila is a complex and plastic trait.

Bing X, Rzezniczak TZ, Bateman JR, Merritt TJ - G3 (Bethesda) (2014)

Bottom Line: We further show that the magnitude of transvection at the Men locus is modified by both genetic background and environment (temperature), demonstrating that transvection is a plastic phenotype.Our results suggest that transvection effects in D. melanogaster are shaped by a dynamic interplay between environment and genetic background.Interestingly, we find that cis-based regulation of the Men gene is more robust to genetic background and environment than trans-based.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada.

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Model of trans-interactions at the Malic enzyme (Men). (A) The D. melanogaster Men locus is on the right arm of the third chromosome (3R) with 5′ region of ~17 kb devoid of other open reading frames. (B) Mean ± SE MEN enzyme activity of MenExi−/MenExi+ heterozygotes. We investigated trans-interactions at this locus using a suite of P-element excision−derived knockout alleles, MenExi−, that drive greater than expected amounts of MEN activity when heterozygous with a functional copy of the Men gene (MenExi−/ MenExi+). Lowercase letters indicate statistical bins of MEN activity for the MenExi− alleles determined by Tukey’s honestly significant difference test after an analysis of covariance using wet weight as a covariate to normalize for possible differences in fly size (data and analysis from Lum and Merritt 2011). (C) Map of MenExi− allele excision sites: MenEx3+ is a perfect excision (used as “normal” or wild-type), the other excision alleles have deletion sizes (represented by dotted line) that range from 500bp to 16kb around the transcription start site (TSS) of Men (see Table S1 for exact descriptions). (D) Model of gene regulation at Men with two functional alleles of the Men gene, interactions are predominantly cis-based. Ovals represent hypothetical transcription factor binding sites, and thin arrows represent interactions between transcription factors and the transcriptional machinery. (E) Model of gene regulation at Men with one functional and one knockout Men allele, interactions are now a combination of cis and trans. Potential synergistic interactions between the enhancers in cis and trans to the functional allele may lead to close to, and sometimes greater than, 100% wild-type MEN activity.
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fig1: Model of trans-interactions at the Malic enzyme (Men). (A) The D. melanogaster Men locus is on the right arm of the third chromosome (3R) with 5′ region of ~17 kb devoid of other open reading frames. (B) Mean ± SE MEN enzyme activity of MenExi−/MenExi+ heterozygotes. We investigated trans-interactions at this locus using a suite of P-element excision−derived knockout alleles, MenExi−, that drive greater than expected amounts of MEN activity when heterozygous with a functional copy of the Men gene (MenExi−/ MenExi+). Lowercase letters indicate statistical bins of MEN activity for the MenExi− alleles determined by Tukey’s honestly significant difference test after an analysis of covariance using wet weight as a covariate to normalize for possible differences in fly size (data and analysis from Lum and Merritt 2011). (C) Map of MenExi− allele excision sites: MenEx3+ is a perfect excision (used as “normal” or wild-type), the other excision alleles have deletion sizes (represented by dotted line) that range from 500bp to 16kb around the transcription start site (TSS) of Men (see Table S1 for exact descriptions). (D) Model of gene regulation at Men with two functional alleles of the Men gene, interactions are predominantly cis-based. Ovals represent hypothetical transcription factor binding sites, and thin arrows represent interactions between transcription factors and the transcriptional machinery. (E) Model of gene regulation at Men with one functional and one knockout Men allele, interactions are now a combination of cis and trans. Potential synergistic interactions between the enhancers in cis and trans to the functional allele may lead to close to, and sometimes greater than, 100% wild-type MEN activity.

Mentions: The D. melanogaster Malic enzyme (Men) gene is developing into a promising system for determination of the molecular mechanisms underlying trans-interactions. Flies heterozygous for small deletion knockout alleles of the Malic enzyme gene (Men) have greater than expected levels of malic enzyme (MEN) protein activity that are not simply physiological up-regulation (Merritt et al. 2005; 2009; Lum and Merritt 2011; Figure 1). Lum and Merritt (2011) used a suite of knockout alleles (MenExi−) with small deletions around the Men transcription start site (Figure 1, B and C) and a set of Men+ third chromosomes extracted from wild populations to demonstrate that the high levels of MEN activity were driven by trans-interaction−dependent up-regulation, and that the amount of increased MEN activity varied with the size and location of the excisions and the genetic background of the fly. The authors suggested that the up-regulation resulted from transvection (Figure 1, D and E). Although the Men regulatory region has not been well characterized, Lum and Merritt (2011) identified a suite of potential regulatory sites in the region computationally and suggested that the experimental differences in trans-effects of alleles with even small differences in their excision may be a function of multiple interacting regulatory sites. Interestingly, the differences in trans-effects caused by different deletion alleles and third chromosomes backgrounds often were subtle, and the significant variations were only detectable because of the sensitivity of the MEN activity assay; activity differences as small as 5% can be reliably distinguished (Merritt et al. 2005, 2009; Lum and Merritt 2011; Rzezniczak and Merritt 2012).


Transvection-based gene regulation in Drosophila is a complex and plastic trait.

Bing X, Rzezniczak TZ, Bateman JR, Merritt TJ - G3 (Bethesda) (2014)

Model of trans-interactions at the Malic enzyme (Men). (A) The D. melanogaster Men locus is on the right arm of the third chromosome (3R) with 5′ region of ~17 kb devoid of other open reading frames. (B) Mean ± SE MEN enzyme activity of MenExi−/MenExi+ heterozygotes. We investigated trans-interactions at this locus using a suite of P-element excision−derived knockout alleles, MenExi−, that drive greater than expected amounts of MEN activity when heterozygous with a functional copy of the Men gene (MenExi−/ MenExi+). Lowercase letters indicate statistical bins of MEN activity for the MenExi− alleles determined by Tukey’s honestly significant difference test after an analysis of covariance using wet weight as a covariate to normalize for possible differences in fly size (data and analysis from Lum and Merritt 2011). (C) Map of MenExi− allele excision sites: MenEx3+ is a perfect excision (used as “normal” or wild-type), the other excision alleles have deletion sizes (represented by dotted line) that range from 500bp to 16kb around the transcription start site (TSS) of Men (see Table S1 for exact descriptions). (D) Model of gene regulation at Men with two functional alleles of the Men gene, interactions are predominantly cis-based. Ovals represent hypothetical transcription factor binding sites, and thin arrows represent interactions between transcription factors and the transcriptional machinery. (E) Model of gene regulation at Men with one functional and one knockout Men allele, interactions are now a combination of cis and trans. Potential synergistic interactions between the enhancers in cis and trans to the functional allele may lead to close to, and sometimes greater than, 100% wild-type MEN activity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232543&req=5

fig1: Model of trans-interactions at the Malic enzyme (Men). (A) The D. melanogaster Men locus is on the right arm of the third chromosome (3R) with 5′ region of ~17 kb devoid of other open reading frames. (B) Mean ± SE MEN enzyme activity of MenExi−/MenExi+ heterozygotes. We investigated trans-interactions at this locus using a suite of P-element excision−derived knockout alleles, MenExi−, that drive greater than expected amounts of MEN activity when heterozygous with a functional copy of the Men gene (MenExi−/ MenExi+). Lowercase letters indicate statistical bins of MEN activity for the MenExi− alleles determined by Tukey’s honestly significant difference test after an analysis of covariance using wet weight as a covariate to normalize for possible differences in fly size (data and analysis from Lum and Merritt 2011). (C) Map of MenExi− allele excision sites: MenEx3+ is a perfect excision (used as “normal” or wild-type), the other excision alleles have deletion sizes (represented by dotted line) that range from 500bp to 16kb around the transcription start site (TSS) of Men (see Table S1 for exact descriptions). (D) Model of gene regulation at Men with two functional alleles of the Men gene, interactions are predominantly cis-based. Ovals represent hypothetical transcription factor binding sites, and thin arrows represent interactions between transcription factors and the transcriptional machinery. (E) Model of gene regulation at Men with one functional and one knockout Men allele, interactions are now a combination of cis and trans. Potential synergistic interactions between the enhancers in cis and trans to the functional allele may lead to close to, and sometimes greater than, 100% wild-type MEN activity.
Mentions: The D. melanogaster Malic enzyme (Men) gene is developing into a promising system for determination of the molecular mechanisms underlying trans-interactions. Flies heterozygous for small deletion knockout alleles of the Malic enzyme gene (Men) have greater than expected levels of malic enzyme (MEN) protein activity that are not simply physiological up-regulation (Merritt et al. 2005; 2009; Lum and Merritt 2011; Figure 1). Lum and Merritt (2011) used a suite of knockout alleles (MenExi−) with small deletions around the Men transcription start site (Figure 1, B and C) and a set of Men+ third chromosomes extracted from wild populations to demonstrate that the high levels of MEN activity were driven by trans-interaction−dependent up-regulation, and that the amount of increased MEN activity varied with the size and location of the excisions and the genetic background of the fly. The authors suggested that the up-regulation resulted from transvection (Figure 1, D and E). Although the Men regulatory region has not been well characterized, Lum and Merritt (2011) identified a suite of potential regulatory sites in the region computationally and suggested that the experimental differences in trans-effects of alleles with even small differences in their excision may be a function of multiple interacting regulatory sites. Interestingly, the differences in trans-effects caused by different deletion alleles and third chromosomes backgrounds often were subtle, and the significant variations were only detectable because of the sensitivity of the MEN activity assay; activity differences as small as 5% can be reliably distinguished (Merritt et al. 2005, 2009; Lum and Merritt 2011; Rzezniczak and Merritt 2012).

Bottom Line: We further show that the magnitude of transvection at the Men locus is modified by both genetic background and environment (temperature), demonstrating that transvection is a plastic phenotype.Our results suggest that transvection effects in D. melanogaster are shaped by a dynamic interplay between environment and genetic background.Interestingly, we find that cis-based regulation of the Men gene is more robust to genetic background and environment than trans-based.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada.

Show MeSH
Related in: MedlinePlus