1
|
Meersseman C, Léjard V, Rebours E, Boussaha M, Maftah A, Petit D, Rocha D. Bovine TWINKLE and mitochondrial ribosomal protein L43 genes are regulated by an evolutionary conserved bidirectional promoter. Gene 2013; 537:154-63. [PMID: 24361965 DOI: 10.1016/j.gene.2013.11.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/30/2013] [Indexed: 11/16/2022]
Abstract
TWINKLE is a mitochondrial DNA helicase playing an important role in mitochondrial DNA replication. In human, mutations in this gene cause progressive external ophtalmoplegia and mitochondrial DNA depletion syndrome-7. TWINKLE is well conserved among multicellular eukaryotes and is believed to be a key regulator of mitochondrial DNA copy number in mammals. Despite its involvement in several diseases and its important function in mitochondrial DNA metabolism, nothing is known about the regulation of the expression of TWINKLE. We have analysed the 5'-flanking genomic region of the bovine TWINKLE gene and found it was localised adjacent to the MRPL43 gene in a head-to-head orientation, suggesting that both genes are regulated by a shared bidirectional promoter. The bovine 75-bp long intergenic region shows substantial homology across different species and contains several conserved putative transcription factor binding sites. A TATA box, however, was lacking. Using a dual fluorescent reporter system and transient transfection assays, we have analysed the bovine intergenic region between TWINKLE and MRPL43. This small genomic fragment showed a bidirectional promoter activity. As the TWINKLE/MRPL43 bidirectional promoter tested was highly conserved, it is likely that the results we obtained here in cattle may be extended to the other species.
Collapse
Affiliation(s)
- Cédric Meersseman
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Véronique Léjard
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Mekki Boussaha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Abderrahman Maftah
- INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Daniel Petit
- INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Dominique Rocha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.
| |
Collapse
|
2
|
Hodar C, Zuñiga A, Pulgar R, Travisany D, Chacon C, Pino M, Maass A, Cambiazo V. Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo. Gene 2013; 535:210-7. [PMID: 24321690 DOI: 10.1016/j.gene.2013.11.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/30/2013] [Accepted: 11/14/2013] [Indexed: 10/25/2022]
Abstract
In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica.
Collapse
Affiliation(s)
- Christian Hodar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Alejandro Zuñiga
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- Laboratorio de Bioinformática y Matemática del Genoma, Center for Mathematical Modeling, FCFM-Universidad de Chile, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Carlos Chacon
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile
| | - Michael Pino
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile
| | - Alejandro Maass
- Laboratorio de Bioinformática y Matemática del Genoma, Center for Mathematical Modeling, FCFM-Universidad de Chile, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile; Department of Mathematical Engineering, FCFM-Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile.
| |
Collapse
|
3
|
Yokoyama S, Starmer WT, Liu Y, Tada T, Britt L. Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes. Gene 2013; 534:93-9. [PMID: 24125953 DOI: 10.1016/j.gene.2013.09.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 01/08/2023]
Abstract
Aquatic organisms such as cichlids, coelacanths, seals, and cetaceans are active in UV-blue color environments, but many of them mysteriously lost their abilities to detect these colors. The loss of these functions is a consequence of the pseudogenization of their short wavelength-sensitive (SWS1) opsin genes without gene duplication. We show that the SWS1 gene (BdenS1ψ) of the deep-sea fish, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years ago (Mya) yet it is still transcribed. The rates of nucleotide substitution (~1.4 × 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes.
Collapse
Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
| | | | | | | | | |
Collapse
|