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Basharat R, de Bruijn SE, Zahid M, Rodenburg K, Hitti-Malin RJ, Rodríguez-Hidalgo M, Boonen EGM, Jarral A, Mahmood A, Corominas J, Khalil S, Zai JA, Ali G, Ruiz-Ederra J, Gilissen C, Cremers FPM, Ansar M, Panneman DM, Roosing S. Next-generation sequencing to genetically diagnose a diverse range of inherited eye disorders in 15 consanguineous families from Pakistan. Exp Eye Res 2024; 244:109945. [PMID: 38815792 DOI: 10.1016/j.exer.2024.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by photoreceptor dysfunction or degeneration. Clinical and phenotypic overlap between IRDs makes the genetic diagnosis very challenging and comprehensive genomic approaches for accurate diagnosis are frequently required. While there are previous studies on IRDs in Pakistan, causative genes and variants are still unknown for a significant portion of patients. Therefore, there is a need to expand the knowledge of the genetic spectrum of IRDs in Pakistan. Here, we recruited 52 affected and 53 normal individuals from 15 consanguineous Pakistani families presenting non-syndromic and syndromic forms of IRDs. We employed single molecule Molecular Inversion Probes (smMIPs) based panel sequencing and whole genome sequencing to identify the probable disease-causing variants in these families. Using this approach, we obtained a 93% genetic solve rate and identified 16 (likely) causative variants in 14 families, of which seven novel variants were identified in ATOH7, COL18A1, MERTK, NDP, PROM1, PRPF8 and USH2A while nine recurrent variants were identified in CNGA3, CNGB1, HGSNAT, NMNAT1, SIX6 and TULP1. The novel MERTK variant and one recurrent TULP1 variant explained the intra-familial locus heterogeneity in one of the screened families while two recurrent CNGA3 variants explained compound heterozygosity in another family. The identification of variants in known disease-associated genes emphasizes the utilization of time and cost-effective screening approaches for rapid diagnosis. The timely genetic diagnosis will not only identify any associated systemic issues in case of syndromic IRDs, but will also aid in the acceleration of personalized medicine for patients affected with IRDs.
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Affiliation(s)
- Rabia Basharat
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Zahid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Erica G M Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Afeefa Jarral
- Department of Biotechnology, Mirpur University of Science and Technology, Mirpur, (AJK), Pakistan
| | - Arif Mahmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sharqa Khalil
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jawaid Ahmed Zai
- Department of Physiology and MLT, University of Sindh, Jamshoro, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Daan M Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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González-Rovira A, Mourente G, Igartuburu JM, Pendon C. Molecular and functional characterization of a SCD 1b from European sea bass (Dicentrarchus labrax L.). Comp Biochem Physiol B Biochem Mol Biol 2021; 258:110698. [PMID: 34801709 DOI: 10.1016/j.cbpb.2021.110698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 10/19/2022]
Abstract
Fatty acid desaturation is a highly complex and regulated process involving different molecular and genetic actors. Ultimally, the fatty acid desaturase enzymes are responsible for the introduction of double bonds at different positions of specific substrates, resulting in a wide variety of mono- and poly-unsaturated fatty acids. This substrate-specificity makes it possible to meet all the functional needs of the different tissues against a wide variety of internal and external conditions, giving rise to a varied profile of expression and functionality of the different desaturases in the body. Being our main interest to study and characterize at the molecular level the fatty acid desaturation process in fishes, we have focused our effort on characterizing SCD 1b from European sea bass (Dicentrarchus labrax, L.). In this work, we have characterized a tearoyl-CoA Desaturase cDNA that codes a protein of 334 amino acids, which shares the greatest homology to marine fish SCD 1b. Northern blot analysis showed two transcripts of 3.5 kb and 1.4 kb. Two putative cis-acting conserved motifs are localized in the cDNA 5'-end: a polypyrimidine CT dinucleotide repeat tract and two non-palindromic putative NRL-response elements (NREs). The deduced protein presents two Δ9 FADs like domain, three His-rich motifs, a total of nine His residues acting as di‑iron coordination ligands. The SCD 1b 3D protein modelling shows a structure made up primarily of α-helices, four of which could be transmembrane helices. The catalytic region is oriented to the cytosolic side of the Endoplasmic Reticulum membrane, where the 9-histidine residues are arranged coordinated to two non-heme Fe2+ ions. A new His-containing motif NX3H-like includes an Asn residue that participates in the coordination of Fe2+1 through a water molecule. The protein has a large pocket with a large opening to the outside. It includes a tunnel in which the substrate-binding site is located. The external shape is reminiscent of a boathook. It shows group specificity, although a greater preference for 18C substrates. The length of the tunnel, delimited by seven amino acids that forms a pocket at the end of the tunnel, the possibility that the substrates adopt different conformations inside the tunnel as well as and the movement of acyl chain inside the tunnel, could explain the high preference for 18C fatty acids and the group specificity of the enzyme. The cDNA encodes a functional SCD enzyme, whose subcellular localization is the Endoplasmic Reticulum, which complements the ole1Δ gene-disrupted gene in DTY-11A Saccharomyces cerevisiae strain and produces an increment of palmitoleic and oleic acids. The scd 1b gene is expressed in all tested tissues, showing the liver and adipose tissue a higher level of expression against the brain, heart, gonad and intestine. Scd 1b expression was always bigger than those of the Δ6 fad gene, being especially significant in adipose tissue and liver. From our data, we conclude that, in contrast to the functional significance of SCD 1b in adipose tissue, liver and heart, Δ6 FAD seems to play a more determining role in the biosynthesis of unsaturated fatty acids in the intestine, brain and gonad in fish.
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Affiliation(s)
- Almudena González-Rovira
- Departamento de Biomedicina, Biotecnología y Salud Pública, INBIO, Facultad de Ciencias, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain.
| | - Gabriel Mourente
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain.
| | - José Manuel Igartuburu
- Departamento de Química Orgánica, INBIO, Facultad de Ciencias, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain.
| | - Carlos Pendon
- Departamento de Biomedicina, Biotecnología y Salud Pública, INBIO, Facultad de Ciencias, Universidad de Cádiz, 11519 Puerto Real, Cádiz, Spain.
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Rathi S, Jalali S, Musada GR, Patnaik S, Balakrishnan D, Hussain A, Kaur I. Mutation spectrum of NDP, FZD4 and TSPAN12 genes in Indian patients with retinopathy of prematurity. Br J Ophthalmol 2017; 102:276-281. [PMID: 28982955 DOI: 10.1136/bjophthalmol-2017-310958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/18/2017] [Accepted: 09/09/2017] [Indexed: 12/18/2022]
Abstract
AIM Retinopathy of prematurity (ROP) is a vasoproliferative eye disease in preterm infants. Based on its phenotypic similarities with familial exudative vitreo retinopathy (FEVR), the present study was conducted to screen the Norrin signalling pathway genes (already been implicated in FEVR) for understanding their involvement among Indian patients with ROP. METHODS The study cohort consisted of patients with ROP (n=246) and controls (n=300) that included full term (n=110) and preterm babies devoid of ROP (n=190). Screening of the NDP, FZD4, TSPAN12 genes were accomplished by resequencing the entire coding and untranslated regions (UTR). The genotype data of the patients with ROP were analysed in the background of their clinical manifestations and further analysed in conjunction with other available data on these genes worldwide. RESULTS Two novel variants in intron 1 (IVS1 +16A>G) and 3'UTR (c.5 22T>C) along with a previously reported change in the 5'UTR (c.395_409del14bp) were observed in the NDP gene in three patients with ROP. Screening of the FZD4 revealed four heterozygous variants, p.(Pro33Ser), p.(Pro168Ser), p.(Ile192Ile) and p.(Ile360Val), a compound heterozygous (p.(Pro33Ser)/p.(Pro168Ser)) and a 3'UTR (c*G>T) variants in the study cohort. Variants p.(Pro33Ser) and p.(Pro168Ser) were found to be significantly associated with ROP. A heterozygous variant p.(Leu119Arg) in TSPAN12 gene was observed in a patient with threshold ROP. However, a formal genotype-phenotype correlation could not be established due to the low frequencies of the variant alleles in these genes. CONCLUSIONS This is a first study that revealed association of few variants in Norrin signalling genes among Indian patients with ROP that warrants further detailed investigation worldwide.
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Affiliation(s)
- Sonika Rathi
- Kallam Anji Reddy Molecular Genetics Laboratory, Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Subhadra Jalali
- Smt Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | - Ganeswara Rao Musada
- Kallam Anji Reddy Molecular Genetics Laboratory, Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Satish Patnaik
- Kallam Anji Reddy Molecular Genetics Laboratory, Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Divya Balakrishnan
- Smt Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | - Anjli Hussain
- Smt Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | - Inderjeet Kaur
- Kallam Anji Reddy Molecular Genetics Laboratory, Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
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Kondo H. Complex genetics of familial exudative vitreoretinopathy and related pediatric retinal detachments. Taiwan J Ophthalmol 2015; 5:56-62. [PMID: 29018668 PMCID: PMC5602728 DOI: 10.1016/j.tjo.2015.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/31/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
Familial exudative vitreoretinopathy (FEVR) is a hereditary vitreoretinal disorder that can cause various types of retinal detachments. The abnormalities in eyes with FEVR are caused by poor vascularization in the peripheral retina. The genetics of FEVR is highly heterogeneous, and mutations in the genes for Wnt signaling and a transcription factor have been reported to be responsible for FEVR. These factors have been shown to be the regulators of the pathophysiological pathways of retinal vascular development. Studies conducted to identify the causative genes of FEVR have uncovered a diverse and complex relationship between FEVR and other diseases; for example, Norrie disease, a Mendelian-inherited disease; retinopathy of prematurity, a multifactorial genetic disease; and Coats disease, a nongenetic disease, associated with pediatric retinal detachments.
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Affiliation(s)
- Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
- Corresponding author. Department of Ophthalmology, University of Occupational and Environmental Health, Number 1-1, Iseigaoka, Yahatanishiku, Kitakyushu 807-8555, Japan. E-mail address:
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Shastry BS. Genetics of familial exudative vitreoretinopathy and its implications for management. EXPERT REVIEW OF OPHTHALMOLOGY 2014. [DOI: 10.1586/eop.12.40] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Zhang XY, Jiang WY, Chen LM, Chen SQ. A novel Norrie disease pseudoglioma gene mutation, c.-1_2delAAT, responsible for Norrie disease in a Chinese family. Int J Ophthalmol 2013; 6:739-43. [PMID: 24392318 DOI: 10.3980/j.issn.2222-3959.2013.06.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/26/2013] [Indexed: 11/02/2022] Open
Abstract
AIM To investigate the genetic findings and phenotypic characteristics of a Chinese family with Norrie disease (ND). METHODS Molecular genetic analysis and clinical examinations were performed on a Chinese family with ND. Mutations in the Norrie disease pseudoglioma (NDP) gene were detected by direct sequencing. Haplotypes were constructed and compared with the phenotypes in the family. Evolutionary comparisons and mutant open reading frame (ORF) prediction were also undertaken. RESULTS Two family members with ocular manifestations were diagnosed with ND. No signs of sensorineural hearing loss were observed in either patient, while one of them showed signs of mild mental retardation. A novel heterozygous mutation in the NDP gene, c.-1_2delAAT, was detected in both patients. The mutation and the mutation bearing haplotype co-segregated with the ND phenotype in males and was transmitted from their mothers and/or grandmothers (II:2). The male without ND did not harbor the mutation. The mutation occurred at the highly conserved nucleotides. ORF finder predicted that the mutation would lead to the production of a truncated protein that lacks the first 11 N-terminal amino acids. CONCLUSION A novel mutation, c.-1_2delAAT in the NDP gene, was identified in a Chinese family with ND. This mutation caused ND without obvious sensorineural hearing loss. Mental disorder was found in one but not the other patients. The clinical heterogeneity in the family indicated that other genetic variants and epigenetic factors may also play a role in the disease presentation.
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Affiliation(s)
- Xin-Yu Zhang
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Wei-Ying Jiang
- Department of Medical Genetics, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Lu-Ming Chen
- Department of Medical Genetics, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Su-Qin Chen
- Department of Medical Genetics, Zhongshan Medical College, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
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Pelcastre EL, Villanueva-Mendoza C, Zenteno JC. Novel and recurrent NDP gene mutations in familial cases of Norrie disease and X-linked exudative vitreoretinopathy. Clin Exp Ophthalmol 2010; 38:367-74. [PMID: 20491809 DOI: 10.1111/j.1442-9071.2010.02245.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PURPOSE To present the results of molecular analysis of the NDP gene in Mexican families with Norrie disease (ND) and X-linked familial exudative vitreoretinopathy (XL-FEVR). METHODS Two unrelated families with ND and two with XL-FEVR were studied. Clinical diagnosis was suspected on the basis of a complete ophthalmologic examination. Molecular methods included DNA isolation from peripheral blood leucocytes, polymerase chain reaction amplification and direct nucleotide sequencing analysis of the complete coding region and exon-intron junctions of NDP. Haplotype analysis using NDP-linked microsatellites markers was performed in both ND families. RESULTS A novel Norrin missense mutation, p.Arg41Thr, was identified in two apparently unrelated families with ND. Haplotype analysis demonstrated that affected males in these two families shared the same ND-linked haplotype, suggesting a common origin for this novel mutation. The previously reported p.Arg121Trp and p.Arg121Gln Norrin mutations were identified in the two families with XL-FEVR. CONCLUSION Our results expand the mutational spectrum in ND. This is the first report of ND resulting from mutation at arginine position 41 of Norrin. Interestingly, mutations at the same residue but resulting in a different missense change were previously described in subjects with XL-FEVR (p.Arg41Lys) or persistent fetal vasculature syndrome (p.Arg41Ser), indicating that the novel p.Arg41Thr change causes a more severe retinal phenotype. Preliminary data suggest a founder effect for the ND p.Arg41Thr mutation in these two Mexican families.
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Affiliation(s)
- Erika L Pelcastre
- Research Unit and Department of Genetics, Institute of Ophthalmology Conde de Valenciana, Chimalpopoca 14, Col. Obrera, Mexico City 06800, Mexico
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Abstract
Single nucleotide polymorphism (SNP) is the simplest form of DNA variation among individuals. These simple changes can be of transition or transversion type and they occur throughout the genome at a frequency of about one in 1,000 bp. They may be responsible for the diversity among individuals, genome evolution, the most common familial traits such as curly hair, interindividual differences in drug response, and complex and common diseases such as diabetes, obesity, hypertension, and psychiatric disorders. SNPs may change the encoded amino acids (nonsynonymous) or can be silent (synonymous) or simply occur in the noncoding regions. They may influence promoter activity (gene expression), messenger RNA (mRNA) conformation (stability), and subcellular localization of mRNAs and/or proteins and hence may produce disease. Therefore, identification of numerous variations in genes and analysis of their effects may lead to a better understanding of their impact on gene function and health of an individual. This improved knowledge may provide a starting point for the development of new, useful SNP markers for medical testing and a safer individualized medication to treat the most common devastating disorders. This will revolutionize the medical field in the future. To illustrate the effect of SNPs on gene function and phenotype, this minireview focuses on evidences revealing the impact of SNPs on the development and progression of three human eye disorders (Norrie disease, familial exudative vitreoretinopathy, and retinopathy of prematurity) that have overlapping clinical manifestations.
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Affiliation(s)
- Barkur S Shastry
- Department of Biological Sciences, Oakland University, Rochester, MI, USA
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Quan Y, Ji ZL, Wang X, Tartakoff AM, Tao T. Evolutionary and transcriptional analysis of karyopherin beta superfamily proteins. Mol Cell Proteomics 2008; 7:1254-69. [PMID: 18353765 DOI: 10.1074/mcp.m700511-mcp200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In eukaryotes, karyopherin beta superfamily proteins mediate nucleocytoplasmic transport of macromolecules. We investigated the evolutionary and transcriptional patterns of these proteins using bioinformatics approaches. No obvious homologs were found in prokaryotes, but an extensive set of beta-karyopherin proteins was found in yeast. Among 14 beta-karyopherins of Saccharomyces cerevisiae, eight corresponded to their human orthologs directly without diversification, two were lost, and the remaining four proteins exhibited gene duplications by different mechanisms. We also identified beta-karyopherin orthologs in Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus tropicalis, Gallus gallus, and Mus musculus. beta-Karyopherins were ubiquitously but nonuniformly expressed in distinct cells and tissues. In yeast and mice, the titer of some beta-karyopherin transcripts appeared to be regulated both during the cell cycle and during development. Further virtual analysis of promoter binding elements suggested that the transcription factors SP1, NRF-2, HEN-1, RREB-1, and nuclear factor Y regulate expression of most beta-karyopherin genes. These findings emphasize new mechanisms in functional diversification of beta-karyopherins and regulation of nucleocytoplasmic transport.
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Affiliation(s)
- Yu Quan
- School of Life Sciences and Key Laboratory for Cell Biology and Tumor Cell Engineering, the Ministry of Education of China, Xiamen University, Xiamen, Fujian 361005, China
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Zhong J, Wang H, Zhang D, Liu B, Wang J. Rice repetitive DNA sequence RRD3: a plant promoter and its application to RNA interference. J Genet Genomics 2007; 34:258-66. [PMID: 17498623 DOI: 10.1016/s1673-8527(07)60027-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 05/17/2006] [Indexed: 11/29/2022]
Abstract
Previously, a moderately repetitive DNA sequence (RRD3) was cloned from rice (Oryza sativa L.) by DNA renaturation kinetics. Sequence analysis revealed several conserved promoter motifs, including four TATA-boxes and a CAAT-box, and promoter activity was shown in Escherichia coli and mammalian expression systems. Here, we inserted the RRD3 fragment into the plant promoter-capture vector, pCAMBIA1391Z, and examined whether the RRD3 fragment has promoter activity in plants. Transgenic tobacco and rice calli both showed beta-glucuronidase (GUS) activity, indicating that RRD3 can act as a promoter in both monocot and dicot plants. Based on the promoter characteristic of RRD3, we designed a plant universal binary vector, pCRiRRD3, which is suitable for performing researches on plant RNA interference. This vector has two multiple cloning sites to facilitate sense and antisense cloning of the target sequence, separated by an intron fragment of 200 bp. The efficiency of the vector for gene silencing was assayed by histochemical and quantitative fluorometric GUS assays in transgenic tobacco. These research results suggested that this plant RNAi vector pCRiRRD3 can effectively perform gene silencing researches on both monocot and dicot plants.
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Affiliation(s)
- Jian Zhong
- National Engineering Center of Cell Products, Amcellgene Co., Ltd., Tianjin 300457, China.
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Dickinson JL, Sale MM, Passmore A, FitzGerald LM, Wheatley CM, Burdon KP, Craig JE, Tengtrisorn S, Carden SM, Maclean H, Mackey DA. Mutations in the NDP gene: contribution to Norrie disease, familial exudative vitreoretinopathy and retinopathy of prematurity. Clin Exp Ophthalmol 2006; 34:682-8. [PMID: 16970763 DOI: 10.1111/j.1442-9071.2006.01314.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND To examine the contribution of mutations within the Norrie disease (NDP) gene to the clinically similar retinal diseases Norrie disease, X-linked familial exudative vitreoretinopathy (FEVR), Coat's disease and retinopathy of prematurity (ROP). METHODS A dataset comprising 13 Norrie-FEVR, one Coat's disease, 31 ROP patients and 90 ex-premature babies of <32 weeks' gestation underwent an ophthalmologic examination and were screened for mutations within the NDP gene by direct DNA sequencing, denaturing high-performance liquid chromatography or gel electrophoresis. Controls were only screened using denaturing high-performance liquid chromatography and gel electrophoresis. Confirmation of mutations identified was obtained by DNA sequencing. RESULTS Evidence for two novel mutations in the NDP gene was presented: Leu103Val in one FEVR patient and His43Arg in monozygotic twin Norrie disease patients. Furthermore, a previously described 14-bp deletion located in the 5' unstranslated region of the NDP gene was detected in three cases of regressed ROP. A second heterozygotic 14-bp deletion was detected in an unaffected ex-premature girl. Only two of the 13 Norrie-FEVR index cases had the full features of Norrie disease with deafness and mental retardation. CONCLUSION Two novel mutations within the coding region of the NDP gene were found, one associated with a severe disease phenotypes of Norrie disease and the other with FEVR. A deletion within the non-coding region was associated with only mild-regressed ROP, despite the presence of low birthweight, prematurity and exposure to oxygen. In full-term children with retinal detachment only 15% appear to have the full features of Norrie disease and this is important for counselling parents on the possible long-term outcome.
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Pauli S, Rothnie HM, Chen G, He X, Hohn T. The cauliflower mosaic virus 35S promoter extends into the transcribed region. J Virol 2004; 78:12120-8. [PMID: 15507598 PMCID: PMC525061 DOI: 10.1128/jvi.78.22.12120-12128.2004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A 60-nucleotide region (S1) downstream of the transcription start site of the cauliflower mosaic virus 35S RNA can enhance gene expression. By using transient expression assays with plant protoplasts, this activity was shown to be at least partially due to the effect of transcriptional enhancers within this region. We identify sequence motifs with enhancer function, which are normally masked by the powerful upstream enhancers of the 35S promoter. A repeated CT-rich motif is involved both in enhancer function and in interaction with plant nuclear proteins. The S1 region can also enhance expression from heterologous promoters.
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Affiliation(s)
- Sandra Pauli
- Friedrich Miescher Institute, P.O. Box 2543, CH-4002 Basel, Switzerland
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Yao X, Hu JF, Li T, Yang Y, Sun Z, Ulaner GA, Vu TH, Hoffman AR. Epigenetic regulation of the taxol resistance-associated gene TRAG-3 in human tumors. ACTA ACUST UNITED AC 2004; 151:1-13. [PMID: 15120907 DOI: 10.1016/j.cancergencyto.2003.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Revised: 08/20/2003] [Accepted: 08/28/2003] [Indexed: 12/31/2022]
Abstract
TRAG-3, originally identified as a taxol resistance-associated gene from an ovarian carcinoma cell line, is upregulated in many human tumors. Like many tumor antigens, TRAG-3 mRNA is not detectable or is expressed at very low levels in normal fetal and adult human tissues except for testis, where TRAG-3 mRNA transcripts are detected abundantly. TRAG-3 mRNA is frequently overexpressed in tumors but is rarely detected in adjacent normal tissues. To delineate the transcriptional regulation of this tumor antigen, we cloned and sequenced the TRAG-3 promoter. A 539-base pair fragment upstream of the initiation site, which contains two unusual CT repeat stretches, was sufficient to drive the maximum activity of a luciferase reporter gene. Sodium bisulfite sequencing of genomic DNA revealed that the amount of DNA methylation in exon 2 and in the promoter regions is inversely correlated with gene expression. In normal tissues, TRAG-3 is hypermethylated and is thus transcriptionally silenced. In those tumors where TRAG-3 is actively transcribed, the TRAG-3 promoter and exon 2 are hypomethylated. Treatment of a TRAG-3-silenced cell line H23 with the demethylating reagent 5-aza-cytosine reduced DNA methylation and induced TRAG-3 expression in a dose-dependent manner. These results indicate that DNA demethylation is an important epigenetic mechanism that regulates the TRAG-3 tumor antigen in human tumors.
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Affiliation(s)
- Xiaoming Yao
- Medical Service, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94305, USA
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Shastry BS, Trese MT. Overproduction and partial purification of the Norrie disease gene product, norrin, from a recombinant baculovirus. Biochem Biophys Res Commun 2004; 312:229-34. [PMID: 14630047 DOI: 10.1016/j.bbrc.2003.09.223] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abnormal vascularization of the peripheral retina and retinal detachment are common clinical characteristics of Norrie disease (ND), familial exudative vitreoretinopathy, Coats' disease, and retinopathy of prematurity. Although little is known about the molecular basis of these diseases, studies have shown that all of these diseases are associated with mutations in the ND gene. In spite of this, little is known about norrin, its molecular mechanism of action, and its functional relationship with the development of abnormal retinal vasculature. To obtain a large quantity of norrin for structural and functional studies, we have overproduced it in insect cells. For this purpose, a cDNA fragment (869 bp) was isolated from a human retinal cDNA library by amplification and was cloned into an expression vector. The purified plasmid was co-transfected with wild-type linearized Bac-N-Blue DNA into S. frugiperda Sf21 insect cells. The recombinant virus plaques were purified and clones were selected based on the level of recombinant protein expressed in Sf21 cells infected with a purified recombinant virus. From these, a high-titer stock was generated and subsequently used to prepare a fused protein on a large scale. The protein was partially purified by the process of immobilized metal affinity chromatography and the use of ion exchange chromatography
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Affiliation(s)
- Barkur S Shastry
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.
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Bizzaro JW, Marx KA. Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA. BMC Bioinformatics 2003; 4:22. [PMID: 12791171 PMCID: PMC165442 DOI: 10.1186/1471-2105-4-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2003] [Accepted: 06/05/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Simple sequence repeats (SSRs), microsatellites or polymeric sequences are common in DNA and are important biologically. From mononucleotide to trinucleotide repeats and beyond, they can be found in long (> 6 repeating units) tracts and may be characterized by quantifying the frequencies in which they are found and their tract lengths. However, most of the existing computer programs that find SSR tracts do not include these methods. RESULTS A computer program named Poly has been written not only to find SSR tracts but to analyze the results quantitatively. CONCLUSIONS Poly is significant in its use of non-standard, quantitative methods of analysis. And, with its flexible object model and data structure, Poly and its generated data can be used for even more sophisticated analyses.
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Affiliation(s)
- Jeff W Bizzaro
- Bioinformatics Organization, Inc., 28 Pope Street, Hudson, MA 01749 USA
- Center for Intelligent Biomaterials, Dept. of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854 USA
| | - Kenneth A Marx
- Center for Intelligent Biomaterials, Dept. of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854 USA
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Duchange N, Saleh MC, de Arriba Zerpa G, Pidoux J, Guillou F, Zakin MM, Baron B. Alternative splicing in the brain of mice and rats generates transferrin transcripts lacking, as in humans, the signal peptide sequence. Neurochem Res 2002; 27:1459-63. [PMID: 12512950 DOI: 10.1023/a:1021692220482] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Transferrin (Tf), the iron-transport protein of vertebrate serum, is mainly synthesized in hepatocytes but is also found in other cell-types including oligodendrocytes. Our laboratory has characterized in a human oligodendrial cell line the presence of a new Tf transcript containing an alternative exon 1b replacing the classical exon 1 and conducting to the elimination of the signal peptide sequence. In this manuscript, we show by RT-PCR and 5'-RACE experiments that alternative transcripts also exist in mouse and rat and are found in brain mRNA preparations. Mouse alternative first exon is homologous to human exon 1b while rat Tf gene was found to use a new first exon named 1c. In all species, the alternative transcript does not contain the signal peptide sequence and possibly encode for a Tf protein devoid of signal peptide showing that this phenomenon is not restricted to human gene. We also present genomic sequence data from the previously unknown 5' genomic rat region, which allowed the alignment of the alternative exons 1 in the three species.
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Affiliation(s)
- Nathalie Duchange
- Unité d'Expression des Gènes Eucaryotes, Institut Pasteur, 28 rue du Dr. Roux, 75015 Paris, France
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