Structural analysis of a 4414-bp element in Drosophila melanogaster

Yu, Bo; Wang, X. T.; Li, H. W.; Zhao, Chunfang; Wu, Chao; Deng, Xuemei

doi:10.4238/vol10-2gmr987

Cited by 3 publications

(3 citation statements)

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“…egg production, egg weight and body weight [35], induce lymphoid or erythroid leukosis and a variety of tumors [35], and cause some phenotype variants, i.e. dilute coat color mutation [36] and hairless mutation in mice [37], recessive white [38], henny-feathering mutation [39], and the sex-linked late-feathering mutation [40] in chickens and outheld wing mutation in Drosophila melanogaster [41]. ERV could alter splicing patterns of transcript to produce variants such as the recessive white mutation in the chickens [38].…”

Section: Discussionmentioning

confidence: 99%

An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken

et al. 2013

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The genetic determination of eggshell coloration has not been determined in birds. Here we report that the blue eggshell is caused by an EAV-HP insertion that promotes the expression of SLCO1B3 gene in the uterus (shell gland) of the oviduct in chicken. In this study, the genetic map location of the blue eggshell gene was refined by linkage analysis in an F2 chicken population, and four candidate genes within the refined interval were subsequently tested for their expression levels in the shell gland of the uterus from blue-shelled and non-blue-shelled hens. SLCO1B3 gene was found to be the only one expressed in the uterus of blue-shelled hens but not in that of non-blue-shelled hens. Results from a pyrosequencing analysis showed that only the allele of SLCO1B3 from blue-shelled chickens was expressed in the uterus of heterozygous hens (O*LC/O*N). SLCO1B3 gene belongs to the organic anion transporting polypeptide (OATP) family; and the OATPs, functioning as membrane transporters, have been reported for the transportation of amphipathic organic compounds, including bile salt in mammals. We subsequently resequenced the whole genomic region of SLCO1B3 and discovered an EAV-HP insertion in the 5′ flanking region of SLCO1B3. The EAV-HP insertion was found closely associated with blue eggshell phenotype following complete Mendelian segregation. In situ hybridization also demonstrated that the blue eggshell is associated with ectopic expression of SLCO1B3 in shell glands of uterus. Our finding strongly suggests that the EAV-HP insertion is the causative mutation for the blue eggshell phenotype. The insertion was also found in another Chinese blue-shelled breed and an American blue-shelled breed. In addition, we found that the insertion site in the blue-shelled chickens from Araucana is different from that in Chinese breeds, which implied independent integration events in the blue-shelled chickens from the two continents, providing a parallel evolutionary example at the molecular level.

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Section: Discussionmentioning

confidence: 99%

An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken

et al. 2013

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“…w1118 was a gift from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. All Drosophila melanogaster lines were maintained on a corn flour, yeast, sugar and agar medium at 24 ± 1 °C 42 . Over a period of eight days, the body weight of each fly was determined within 24 hours after eclosion using an electronic balance with an accuracy of 0.000001 g. Rate of heterosis (RH) was calculated to evaluate heterosis in body weight according to the following equation: RH = [(F1−(P1 + P2)/2)/(P1 + P2)/2] × 100%, where F1, P1 and P2 are the average body-weight of the F1 hybrid and the two parental inbreds, respectively.…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster

et al. 2016

Sci Rep

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We observed heteroses for body weight in Drosophila melanogaster after generating hybrids from three inbred lines. To better understand the mechanism for this phenomenon at the mRNA level, we compared the mRNA profiles of the parental and hybrid lines using high-throughput RNA-seq. A total of 5877 differentially expressed genes (DEGs) were found and about 92% of these exhibited parental expression level dominance. Genes in the dominance category were functionally characterized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene classifications offered by the Gene Ontology (GO) Consortium. The analysis identified genes associated with crucial processes such as development and growth in all three crosses. Functional assignments involving aminoglycan metabolism, starch and sucrose metabolism, and galactose metabolism are significantly overrepresented amongst the 215 common dominance DEGs. We conclude that dominance DEGs are important in heteroses in Drosophila melanogaster and contribute specifically to body weight heterosis.

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“…Third, sequences that are not annotated in Flybase but had some limited sequence identity with ZAM and Tirant fragments correspond in fact to a newly identified element that we named Agoriino and a Pifo element. Pifo was previously identified in Drosophila yakuba (20) and a 4,414-bp degenerate Pifo in D. melanogaster (21). Consequently, only one vestige of ZAM is present at position X:21649838..21655021.…”

Section: In Silico Analysis Of the Flam Locus Reveals A Large Number mentioning

confidence: 99%

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

Zanni

Eymery

Coiffet

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

117

159

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Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.RNAi | gene silencing | epigenetics O ver the course of evolution, transposable elements (TEs) have accumulated in the genomes of eukaryotes, where they can account for up to 85% of the DNA (1). Most of these sequences have lost their ability to transpose. They are now stable components of the genomes. Their conservation throughout evolution suggests that they may confer advantageous effects to their hosts. However, transposition of the copies that remain functional could generate deleterious mutations if they were not severely repressed by their host. RNAi, which is a gene-silencing mechanism triggered by small RNAs (reviewed in ref.2), has been identified as being the main cellular machinery involved in the "taming" of TEs (reviewed in refs. 3-5). RNAi pathways involve small RNAs of diverse families. Among them, Piwiinteracting RNAs (piRNAs) have been shown to be involved in TE silencing in the Drosophila ovary. These piRNAs, 23-29 nt long, are bound by the Argonaute proteins Piwi, Argonaute 3, or Aubergine. They are produced by discrete genomic loci named piRNA clusters, which have been described as containing vestiges of TEs (6). One of these loci, the flamenco (flam) locus, extends over 180 kilobases (kb) on the Drosophila X chromosome. It is proximal to the DISCO interacting protein 1 gene (DIP1) and close to pericentromeric heterochromatin. Before the identification of piRNAs, this locus had been shown to regulate the Gypsy retrotransposon (7, 8 (6) showed the potential for the flam cluster to pr...

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Structural analysis of a 4414-bp element in Drosophila melanogaster

Cited by 3 publications

References 39 publications

An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken

An EAV-HP Insertion in 5′ Flanking Region of SLCO1B3 Causes Blue Eggshell in the Chicken

Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

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