Trans-acting Regulatory Locus Research Articles

Trans-eQTL hotspots shape complex traits by modulating cellular states.

Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae. We discovered thousands of genetic correlations between gene expression and growth, suggesting potential functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans-acting regulatory loci. Trans-acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits, but with heterogeneous direction of effect. Our results reveal how trans-acting regulatory hotspots shape complex traits by altering cellular states.

Mapping of a trans-acting regulatory locus of Bone gamma carboxyglutamate protein-related sequence 1 (Bglap-rs1) mRNA levels in mouse chromosome substitution strains

Mapping of a trans-acting regulatory locus of Bone gamma carboxyglutamate protein-related sequence 1 (Bglap-rs1) mRNA levels in mouse chromosome substitution strains

Characterization of regulatory mutations causing anaerobic derepression of the sodA gene in Escherichia coli K12: cooperation between cis- and trans-acting regulatory loci.

The genetic loci leading to anaerobic derepression of a sodA::lacZ protein fusion in a UV-generated mutant strain (UV14) of Escherichia coli were identified. The mutant (UV14) was found to harbour two altered loci: one is in the trans-regulatory gene fnr (fumarate nitrate reduction) where leucine-129 was changed to glutamine (fnr14), and the second (sodA14) is in the promoter region (cis) of the sodA gene apparently affecting the binding of the Fur (ferric uptake regulation) protein. Introduction of an fnr+ gene into UV14 restored anaerobic repression of sodA::lacZ and restored the ability of the cells to reduce nitrate. However, when either the fnr14 or the sodA14 mutation was introduced into an otherwise wild-type background, only slight anaerobic derepression of sodA was observed. When both the cis- and trans-acting mutations (i.e. sodA14 and fnr14) were combined simultaneously in an otherwise wild-type background, the specific activity of sodA::lacZ expression was comparable to that of the original mutant strain (UV14). Furthermore, a genetically confirmed fur fnr double mutant was also similarly derepressed in anaerobic sodA::lacZ expression. The data presented suggest that the cis-mutation in UV14 (sodA14) affects the Fur-binding site in the sodA promoter, while having no effect on Fnr or Arc mediated repression. Also, a second putative Fnr-binding site that straddles the ribosomal binding-site was identified in the sodA gene.

A trans-acting locus regulates transcriptional repression of the female-specific steroid 15 alpha-hydroxylase gene in male mice.

Steroid 15 alpha-hydroxylase (P450(15 alpha)) is a female-specific enzyme in the livers of many inbred mice including DBA/2J. Run-on assays using liver nuclei from GH-deficient Little mice indicated that the P450(15 alpha) gene is transcriptionally repressed by GH in male mice. BALB/cJ is a variant strain in which the gene is expressed in the males as well as in the females. Genetic crosses between DBA/2J and BALB/cJ indicated that expression of the P450(15 alpha) gene in BALB/cJ males is inherited as a recessive trait and is regulated by a single locus. The parental origin of the P450(15 alpha) genes, determined using restriction site polymorphism in the exons of the P450(15 alpha) genes, divided the F2 males expressing the P450(15 alpha) gene into three phenotypes at a ratio of 1:1:2, the individuals expressing the gene from only BALB/cJ or DBA/2J and the individuals expressing the genes from both parents respectively. The results indicate that the repression of the P450(15 alpha) gene in male mice is regulated by a trans-acting regulatory locus between the DBA/2J and BALB/cJ pairs. Because hypophysectomy derepressed the P450(15 alpha) gene in F1 males and GH repressed the gene in hypophysectomized F1 males, the hormone appears to regulate gene repression through a trans-acting locus, named GH-dependent repression, GDR.

Genetic and molecular evidence for a trans-acting regulatory locus controlling glutathione S-transferase-2 expression in Aedes aegypti.

The amount of glutathione S-transferase-2 (GST-2) protein and enzyme activity in a mutant strain (strain GG) of the yellow fever mosquito (Aedes aegypti) is approximately 25-fold higher than in the wild-type (++) strain. The mode of inheritance of the GG phenotype was studied in F1 and backcross progeny using GST enzyme assays, isozyme-specific antisera, and Northern blot analysis. Enzyme assay of parental and F1 progeny showed that the ++ phenotype was dominant to the GG phenotype. This was true for larvae as well as for all tissues examined in adults in both sexes. Immunoblotting experiments showed that, like the ++ strain, F1 larvae and adults express very low levels of GST-2 protein compared with the GG strain. Northern blotting experiments showed that the steady-state levels of GST-2 mRNA in parental and F1 hybrid larvae closely matched the enzyme activity and immunological data. These results suggest the existence of a trans-acting regulatory locus that acts to repress GST-2 mRNA transcription and/or decrease GST-2 mRNA stability in ++ and F1 hybrids. GST enzyme activity in backcross progeny, however, did not segregate into the two distinct phenotypes (low and high) predicted for a single locus, dominant allele model. Backcross progeny expressed a wide range of GST activity and GST-2 protein amount with no apparent fit to simple Mendelian ratios. These backcross data suggest that additional loci are also involved in regulating GST-2 isozyme expression.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular cloning of genes encoding transcription factors with the use of recognition site probes.

In genetically tractable prokaryotes and eukaryotes, most DNA binding transcription factors have been identified as the products of trans-acting regulatory loci. In many complex eukaryotic organisms a similar approach to their identification has not been possible. Instead the recent application of sensitive DNA binding assays, in particular DNase I footprinting (1) and gel electrophoresis of protein-DNA complexes (2,3) has led to the detection and characterization of numerous transcription factors. Each of these proteins binds selectively to a distinctive transcriptional control element and is thereby implicated in regulating the activity of target genes containing such an element (4). The isolation of molecular clones encoding transcription factors facilitates a genetic cum biochemical analysis of their structural and functional properties. Prior to the application of the cloning strategy described below, genes encoding transcription factors could be isolated only by screening recombinant DNA libraries with antibody (5–7) or oligonucleotide probes (6,8,9). The latter are generated from partial amino acid sequences of the relevant proteins. Both screening strategies are dependent on the availability of substantial amounts of the purified transcription factor.

Analysis of Bordetella pertussis virulence gene regulation by use of transcriptional fusions in Escherichia coli

The virulence regulon of Bordetella pertussis includes a trans-acting regulatory locus, bvg, that is required for expression of several virulence factors. The virulence control system also responds to environmental signals. We have reconstructed a bvg-dependent regulatory system in Escherichia coli by using bacteriophage lambda vectors carrying transcriptional fusions to lacZYA. Single-copy lacZYA fusions to the B. pertussis fhaB locus, which encodes the attachment factor filamentous hemagglutinin, were activated nearly 400-fold by pBR322 replicons carrying sequences that included bvg. In contrast, bvg had no effect on the pertussis toxin operon (ptxA-E) promoter in E. coli as measured by ptxA-lacZ expression. Environmental signals that modulate expression of virulence genes in B. pertussis had a pronounced effect on bvg-mediated activation of fhaB-lacZ. MgSO4, nicotinic acid, and low temperature resulted in decreases in beta-galactosidase activities of 175-, 115-, and 45-fold respectively. Sensory transduction and transcriptional activation were tightly coupled, and both required an intact bvg locus as determined by 5' and 3' deletions that eliminated both activities.

Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2-HAP3-responsive site.

We analyzed upstream activation sequence 2 (UAS2), one of two independent UAS elements in the CYC1 gene of Saccharomyces cerevisiae. Deletions and linker scanning mutations across the 87 base pairs previously defined as UAS2 showed two separate functional elements required for full activity. Region 1, from -230 to -200, contains the principal activation site and responds to the trans-acting regulatory loci HAP2 and HAP3. A portion of region 1 is homologous to two other HAP2-HAP3-responsive UASs and includes the G----A transition mutation UP1, which increases UAS2 activity. This consensus sequence TNATTGGT bears striking similarity to several CAAT box sequences of higher cells. Region 2, from -192 to -178, substantially enhances the activity of region 1, yet has little activity by itself. These regions bind distinct proteins found in crudely fractionated yeast extracts.

Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2-HAP3-responsive site.

We analyzed upstream activation sequence 2 (UAS2), one of two independent UAS elements in the CYC1 gene of Saccharomyces cerevisiae. Deletions and linker scanning mutations across the 87 base pairs previously defined as UAS2 showed two separate functional elements required for full activity. Region 1, from -230 to -200, contains the principal activation site and responds to the trans-acting regulatory loci HAP2 and HAP3. A portion of region 1 is homologous to two other HAP2-HAP3-responsive UASs and includes the G----A transition mutation UP1, which increases UAS2 activity. This consensus sequence TNATTGGT bears striking similarity to several CAAT box sequences of higher cells. Region 2, from -192 to -178, substantially enhances the activity of region 1, yet has little activity by itself. These regions bind distinct proteins found in crudely fractionated yeast extracts.

Structure of the transcriptionally repressed phosphate-repressible acid phosphatase gene (PHO5) of Saccharomyces cerevisiae.

We developed a high-copy-number plasmid system containing the entire structural and regulatory sequences of the phosphate-repressible acid phosphatase (PHO5) gene and the TRP1/ARS1 replicator sequences of the yeast Saccharomyces cerevisiae to investigate the mechanism of repression-derepression of transcription. The resulting plasmid was used to transform either wild-type cells or a number of strains which contain mutations in various trans-acting regulatory loci for the production of acid phosphatase. Results of analysis of mRNA levels isolated from the transformed strains grown under repressed or derepressed conditions suggested that normal transcriptional regulation of the gene persisted, although gene copy number was significantly increased. Analysis of changes in linking number (i.e., the number of negative supercoils) of the plasmid isolated under repressed and derepressed growth conditions revealed that the transcriptionally inactive plasmid contained approximately three more negative supercoils than the transcriptionally active plasmid. This difference in topological state was similarly seen in a plasmid containing a sequence-related acid phosphatase gene (PHO11) under the same regulatory control system, but it was not seen in plasmids isolated from some strains containing mutations which caused either fully constitutive or nonderepressible production of acid phosphatase. Finally, analysis of the nucleosome positioning along the inactive gene sequence revealed that an abnormally broad internucleosomal spacer is present in a region presumed to function in the regulation of transcription by the level of Pi in the growth media.

Structure of the transcriptionally repressed phosphate-repressible acid phosphatase gene (PHO5) of Saccharomyces cerevisiae.

We developed a high-copy-number plasmid system containing the entire structural and regulatory sequences of the phosphate-repressible acid phosphatase (PHO5) gene and the TRP1/ARS1 replicator sequences of the yeast Saccharomyces cerevisiae to investigate the mechanism of repression-derepression of transcription. The resulting plasmid was used to transform either wild-type cells or a number of strains which contain mutations in various trans-acting regulatory loci for the production of acid phosphatase. Results of analysis of mRNA levels isolated from the transformed strains grown under repressed or derepressed conditions suggested that normal transcriptional regulation of the gene persisted, although gene copy number was significantly increased. Analysis of changes in linking number (i.e., the number of negative supercoils) of the plasmid isolated under repressed and derepressed growth conditions revealed that the transcriptionally inactive plasmid contained approximately three more negative supercoils than the transcriptionally active plasmid. This difference in topological state was similarly seen in a plasmid containing a sequence-related acid phosphatase gene (PHO11) under the same regulatory control system, but it was not seen in plasmids isolated from some strains containing mutations which caused either fully constitutive or nonderepressible production of acid phosphatase. Finally, analysis of the nucleosome positioning along the inactive gene sequence revealed that an abnormally broad internucleosomal spacer is present in a region presumed to function in the regulation of transcription by the level of Pi in the growth media.

Specific regulation of transcription of the discoidin gene family in Dictyostelium discoideum.

Dictyostelium discoideum strains that carry the dis mutations fail to express the family of developmentally regulated discoidin lectin genes during morphogenesis. We show here that this absence of discoidin lectin expression is due to the failure to transcribe the discoidin genes. Furthermore, the dis mutations appear to affect only discoidin expression and not the expression of other proteins during development, as assessed by a two-dimensional gel analysis of pulse-labeled proteins and by the accumulation of developmentally regulated enzymes. The dis mutations appear to define trans-acting regulatory loci, the products of which act at the transcriptional level to control specifically the developmental expression of the discoidin gene family.

Specific regulation of transcription of the discoidin gene family in Dictyostelium discoideum.

Dictyostelium discoideum strains that carry the dis mutations fail to express the family of developmentally regulated discoidin lectin genes during morphogenesis. We show here that this absence of discoidin lectin expression is due to the failure to transcribe the discoidin genes. Furthermore, the dis mutations appear to affect only discoidin expression and not the expression of other proteins during development, as assessed by a two-dimensional gel analysis of pulse-labeled proteins and by the accumulation of developmentally regulated enzymes. The dis mutations appear to define trans-acting regulatory loci, the products of which act at the transcriptional level to control specifically the developmental expression of the discoidin gene family.