DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio).

Izsvák, Zsuzsanna; Ivics, Zoltán; Garcia-Estefania, David; Fahrenkrug, Scott C.; Hackett, Perry B.

doi:10.1073/pnas.93.3.1077

Cited by 66 publications

(40 citation statements)

References 24 publications

(38 reference statements)

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“…Injection of AANAT2( -1237/-300)-EGFP-PRDM (Fig. 3A), which contains 726 bp of the proximal and distal promoter and lacks a region of repetitive DANA sequences (Izsvak et al 1996), resulted in high levels of pineal EGFP expression (82%) and reduced ectopic expression (30%), similar to the wild-type construct (AANAT2-EGFP-PRDM; Fig. 3B).…”

Section: Functional Characterization Of the Aanat2 Promoter In Vivomentioning

confidence: 98%

Zebrafish arylalkylamine-N-acetyltransferase genes – targets for regulation of the circadian clock

Appelbaum

Vallone²,

Anzulovich³

et al. 2006

Journal of Molecular Endocrinology

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Daily rhythms of melatonin production are controlled by changes in the activity of arylalkylamine-N-acetyltransferase (AANAT). Zebrafish possess two aanats, aanat1 and aanat2; the former is expressed only in the retina and the latter is expressed in both the retina and the pineal gland. Here, their differential expression and regulation were studied using transcript quantification and transient and stable in vivo and in vitro transfection assays. In the pineal gland, the aanat2 promoter exhibited circadian clock-controlled activity, as indicated by circadian rhythms of Enhanced green fluorescent protein (EGFP) mRNA in AANAT2:EGFP transgenic fish. In vivo transient expression analyses of the aanat2 promoter indicated that E-box and photoreceptor conserved elements (PCE) are required for expression in the pineal gland. In the retina, the expression of both genes was characterized by a robust circadian rhythm of their transcript levels. In constant darkness, the rhythmic expression of retinal aanat2 persisted while the aanat1 rhythm disappeared; indicating that the former is controlled by a circadian clock and the latter is also light driven. In the light-entrainable clock-containing PAC-2 zebrafish cell line, both stably transfected aanat1 and aanat2 promoters exhibited a clock-controlled circadian rhythm, characteristic for an E-box-driven expression. Transient co-transfection experiments in NIH-3T3 cells revealed that the two, E-box-and PCE-containing, promoters are driven by the synergistic action of BMAL/CLOCK and orthehodenticle homeobox 5. This study has revealed a shared mechanism for the regulation of two related genes, yet describes their differential phases and photic responses which may be driven by other gene-specific regulatory mechanisms and tissue-specific transcription factor profiles.

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Section: Functional Characterization Of the Aanat2 Promoter In Vivomentioning

confidence: 98%

Zebrafish arylalkylamine-N-acetyltransferase genes – targets for regulation of the circadian clock

Appelbaum

Vallone²,

Anzulovich³

et al. 2006

Journal of Molecular Endocrinology

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“…This could indicate that insertion occurred by combining different repeated sequences. In Danio a retroelement inserted in the intron of the elf-4E gene is also composed by association of a DANA-transposable element with other repetitive sequences (40).…”

Section: Discussionmentioning

confidence: 99%

Zebrafish Acetylcholinesterase Is Encoded by a Single Gene Localized on Linkage Group 7

Bertrand¹,

Chatonnet²,

Takke³

et al. 2001

Journal of Biological Chemistry

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We cloned and sequenced the acetylcholinesterase gene and cDNA of zebrafish, Danio rerio. We found a single gene (ache) located on linkage group LG7. The relative organization of ache, eng2, and shh genes is conserved between zebrafish and mammals and defines a synteny. Restriction fragment length polymorphism analysis was allowed to identify several allelic variations. We also identified two transposable elements in non-coding regions of the gene. Compared with other vertebrate acetylcholinesterase genes, ache gene contains no alternative splicing at 5 or 3 ends where only a T exon is present. The translated sequence is 60 -80% identical to acetylcholinesterases of the vertebrates and exhibits an extra loop specific to teleosts. Analysis of molecular forms showed a transition, at the time of hatching, from the globular G4 form to asymmetric A12 form that becomes prominent in adults. In situ hybridization and enzymatic activity detection on whole embryos confirmed early expression of the acetylcholinesterase gene in nervous and muscular tissues. We found no butyrylcholinesterase gene or activity in Danio. These findings make zebrafish a promising model to study function of acetylcholinesterase during development and regulation of molecular forms assembly in vivo.

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“…Some of these elements are capable of natural insertional mutagenesis (Izsvak et al, 1996;Koga et al, 1996). In order to understand the evolution of TEs in the vertebrate lineage, comparisons between teleost fish and mammalian genomes have been performed particularly for reverse transcriptase retroelements .…”

Section: Diversity Of Transposable Elements (Tes) In Fishmentioning

confidence: 99%

Genome evolution and biodiversity in teleost fish

2004

Heredity

591

430

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Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre-and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates. Heredity (2005) 94, 280-294.

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DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio).

Cited by 66 publications

References 24 publications

Zebrafish arylalkylamine-N-acetyltransferase genes – targets for regulation of the circadian clock

Zebrafish arylalkylamine-N-acetyltransferase genes – targets for regulation of the circadian clock

Zebrafish Acetylcholinesterase Is Encoded by a Single Gene Localized on Linkage Group 7

Genome evolution and biodiversity in teleost fish

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