Expression of tandem gene duplicates is often greater than twofold

Abstract

Tandem gene duplication is an important mutational process in evolutionary adaptation and human disease. Hypothetically, two tandem gene copies should produce twice the output of a single gene, but this expectation has not been rigorously investigated. Here, we show that tandem duplication often results in more than double the gene activity. A naturally occurring tandem duplication of the Alcohol dehydrogenase (Adh) gene exhibits 2.6-fold greater expression than the single-copy gene in transgenic Drosophila. This tandem duplication also exhibits greater activity than two copies of the gene in trans, demonstrating that it is the tandem arrangement and not copy number that is the cause of overactivity. We also show that tandem duplication of an unrelated synthetic reporter gene is overactive (2.3- to 5.1-fold) at all sites in the genome that we tested, suggesting that overactivity could be a general property of tandem gene duplicates. Overactivity occurs at the level of RNA transcription, and therefore tandem duplicate overactivity appears to be a previously unidentified form of position effect. The increment of surplus gene expression observed is comparable to many regulatory mutations fixed in nature and, if typical of other genomes, would shape the fate of tandem duplicates in evolution.

Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

“…DNA coding sequences of alleles that differed in their protein sequence were aligned using MUSCLE and a maximum likelihood phylogeny was inferred in PhyML (v. 3.0) using the best-fit parameters and model TrN + G (Tamura-Nei with gamma-distributed among-site rate variation), as determined by the Akaike information criterion (jModelTest software, v. 2.1.7). Ancestral sequence reconstruction was performed using the maximum likelihood method 48 in PAML software (v. 4.8); sequences were analysed using the GY94 general codon model, with model = 0, nssites = 1, 3 × 4 codon frequencies and a transition/transversion ratio inferred from the data. The posterior probability distribution of ancestral states at each site was analysed at nodes that correspond AncMS and to the last common ancestor of all D. melanogaster alleles.…”

“…ADH enzyme activity from transgenic flies was measured from crude fly homogenates using the ‘manual grinders’ protocol 48 . For each transformation strain, we propagated three replicate cultures (broods), each of which was initiated by placing five females and two males in a vial of yeast-free food to lay eggs for two to three days.…”

“…When males in a vial reached four days old, two flies were collected and homogenized using a Potter–Elvehjem homogenizer in 400 μl of 0.1 M sodium phosphate buffer, pH 8.6, then centrifuged at 21000 × g for 5 min at 4 °C; supernatant from the homogenate of each vial was split among three replicate enzyme assays and three replicate protein concentration assays. Assays for ADH enzyme activity and protein concentration (Quant-IT protein assay, Thermo-Fisher) were performed 48 . Maximal reaction velocity ( V max ) was measured using ethanol and NAD + concentrations more than twice those needed to generate maximum rates.…”

Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

“…Duplicated gene copies can not only change the sequence of their coding region, but can also alter their expression patterns. Duplicated genes in Drosophila have as much as five times greater expression than single copy genes (Loehlin & Carroll, ), with slightly lower rates of expression observed in Caenorhabditis elegans (Konrad et al, ). However, in Drosophila yakuba and some mammalian species, there is little evidence for increased expression following gene duplication (Guschanski, Warnefors, & Kaessmann, ; Henrichsen et al, ; Rogers, Shao, & Thornton, ).…”

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

“…We discover a novel cohort of nuclear circRNAs, enriched at tandem duplicated genes in the zebrafish genome ("tandem-circRNAs"). Although it is already known that the zebrafish genome has undergone a significantly higher rate of tandem duplications compared to other teleost species 15 , this phenomenon and its secondary regulatory effects on gene expression has until recently only been described in Drosophila 16,17,18 and in mammals 19 . Using our newly-developed screen-and-sequence circRNA pipeline, we describe and validate two novel "tandem-circRNAs", circ-cyt1 and circ-smyhc, and show that the splicing events across neighbouring tandem duplicated genes leading to their circularisation are correlative of the formation of chimaeric linear transcripts between the same tandem duplicated genes, echoing a previous observation in Drosophila yakuba 18 .…”