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Wright CF, Sharp LN, Jackson L, Murray A, Ware JS, MacArthur DG, Rehm HL, Patel KA, Weedon MN. Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts. Nat Genet 2024:10.1038/s41588-024-01842-3. [PMID: 39075210 DOI: 10.1038/s41588-024-01842-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/24/2024] [Indexed: 07/31/2024]
Abstract
Penetrance is the probability that an individual with a pathogenic genetic variant develops a specific disease. Knowing the penetrance of variants for monogenic disorders is important for counseling of individuals. Until recently, estimates of penetrance have largely relied on affected individuals and their at-risk family members being clinically referred for genetic testing, a 'phenotype-first' approach. This approach substantially overestimates the penetrance of variants because of ascertainment bias. The recent availability of whole-genome sequencing data in individuals from very-large-scale population-based cohorts now allows 'genotype-first' estimates of penetrance for many conditions. Although this type of population-based study can underestimate penetrance owing to recruitment biases, it provides more accurate estimates of penetrance for secondary or incidental findings. Here, we provide guidance for the conduct of penetrance studies to ensure that robust genotypes and phenotypes are used to accurately estimate penetrance of variants and groups of similarly annotated variants from population-based studies.
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Affiliation(s)
- Caroline F Wright
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
| | - Luke N Sharp
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Leigh Jackson
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Anna Murray
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - James S Ware
- National Heart and Lung Institute and MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
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2
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McVeigh P, McCammick E, Robb E, Brophy P, Morphew RM, Marks NJ, Maule AG. Discovery of long non-coding RNAs in the liver fluke, Fasciola hepatica. PLoS Negl Trop Dis 2023; 17:e0011663. [PMID: 37769025 PMCID: PMC10564125 DOI: 10.1371/journal.pntd.0011663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Long non-coding (lnc)RNAs are a class of eukaryotic RNA that do not code for protein and are linked with transcriptional regulation, amongst a myriad of other functions. Using a custom in silico pipeline we have identified 6,436 putative lncRNA transcripts in the liver fluke parasite, Fasciola hepatica, none of which are conserved with those previously described from Schistosoma mansoni. F. hepatica lncRNAs were distinct from F. hepatica mRNAs in transcript length, coding probability, exon/intron composition, expression patterns, and genome distribution. RNA-Seq and digital droplet PCR measurements demonstrated developmentally regulated expression of lncRNAs between intra-mammalian life stages; a similar proportion of lncRNAs (14.2%) and mRNAs (12.8%) were differentially expressed (p<0.001), supporting a functional role for lncRNAs in F. hepatica life stages. While most lncRNAs (81%) were intergenic, we identified some that overlapped protein coding loci in antisense (13%) or intronic (6%) configurations. We found no unequivocal evidence for correlated developmental expression within positionally correlated lncRNA:mRNA pairs, but global co-expression analysis identified five lncRNA that were inversely co-regulated with 89 mRNAs, including a large number of functionally essential proteases. The presence of micro (mi)RNA binding sites in 3135 lncRNAs indicates the potential for miRNA-based post-transcriptional regulation of lncRNA, and/or their function as competing endogenous (ce)RNAs. The same annotation pipeline identified 24,141 putative lncRNAs in F. gigantica. This first description of lncRNAs in F. hepatica provides an avenue to future functional and comparative genomics studies that will provide a new perspective on a poorly understood aspect of parasite biology.
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Affiliation(s)
- Paul McVeigh
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Erin McCammick
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Emily Robb
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Peter Brophy
- Department of Life Sciences, Aberystwyth University, Wales, United Kingdom
| | - Russell M. Morphew
- Department of Life Sciences, Aberystwyth University, Wales, United Kingdom
| | - Nikki J. Marks
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Aaron G. Maule
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
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3
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Romdhane L, Bouhamed H, Ghedira K, Ben Hamda C, Louhichi A, Jmel H, Romdhane S, Charfeddine C, Mokni M, Abdelhak S, Rebai A. The morbid cutaneous anatomy of the human genome revealed by a bioinformatic approach. Genomics 2020; 112:4232-4241. [PMID: 32650097 DOI: 10.1016/j.ygeno.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 03/28/2020] [Accepted: 07/02/2020] [Indexed: 01/05/2023]
Abstract
Computational approaches have been developed to prioritize candidate genes in disease gene identification. They are based on different pieces of evidences associating each gene with the given disease. In this study, 648 genes underlying genodermatoses have been compared to 1808 genes involved in other genetic diseases using a bioinformatic approach. These genes were studied at the structural, evolutionary and functional levels. Results show that genes underlying genodermatoses present longer CDS and have more exons. Significant differences were observed in nucleotide motif and amino-acid compositions. Evolutionary conservation analysis revealed that genodermatoses genes have less paralogs, more orthologs in Mouse and Dog and are less conserved. Functional analysis revealed that genodermatosis genes seem to be involved in immune system and skin layers. The Bayesian network model returned a rate of good classification of around 80%. This computational approach could help investigators working in the field of dermatology by prioritizing positional candidate genes for mutation screening.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; Department of Biology, Faculty of Sciences of Bizerte, Jarzouna, Université Tunis Carthage, Tunis, Tunisia.
| | - Heni Bouhamed
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Amel Louhichi
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Haifa Jmel
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Chérine Charfeddine
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; High Institut of Biotechnology of Sidi Thabet, University of Manouba, BiotechPole of Sidi Thabet, Ariana, Tunisia
| | - Mourad Mokni
- Department of Dermatology, CHU La Rabta Tunis, Tunis, Tunisia; Public health and infection Research Laboratory, La Rabta Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ahmed Rebai
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
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Chen CH, Pan CY, Lin WC. Overlapping protein-coding genes in human genome and their coincidental expression in tissues. Sci Rep 2019; 9:13377. [PMID: 31527706 PMCID: PMC6746723 DOI: 10.1038/s41598-019-49802-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/29/2019] [Indexed: 01/23/2023] Open
Abstract
The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5'-tandem overlapping and 3'-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.
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Affiliation(s)
- Chao-Hsin Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C
| | - Chao-Yu Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan R.O.C
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan R.O.C.. .,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan R.O.C..
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6
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Mathiasen L, Valentini E, Boivin S, Cattaneo A, Blasi F, Svergun DI, Bruckmann C. The flexibility of a homeodomain transcription factor heterodimer and its allosteric regulation by DNA binding. FEBS J 2016; 283:3134-54. [PMID: 27390177 DOI: 10.1111/febs.13801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Transcription factors are known to modify the DNA that they bind. However, DNA can also serve as an allosteric ligand whose binding modifies the conformation of transcriptional regulators. Here, we describe how heterodimer PBX1:PREP1, formed by proteins playing major roles in embryonic development and tumorigenesis, undergoes an allosteric transition upon DNA binding. We demonstrate through a number of biochemical and biophysical methods that PBX1:PREP1 exhibits a structural change upon DNA binding. Small-angle X-ray scattering (SAXS), circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis demonstrate a different shape, α-helical content, thermodynamic behavior, and solution environment of the holo-complex (with DNA) compared to the apo-complex (without DNA). Given that PBX1 as such does not have a defined DNA selectivity, structural changes upon DNA binding become major factors in the function of the PBX1:PREP1 complex. The observed changes are mapped at both the amino- and carboxy-terminal regions of the two proteins thereby providing important insights to determine how PBX1:PREP1 dimer functions. DATABASE Small-angle scattering data are available in SASBDB under accession numbers SASDAP7, SASDAQ7, and SASDAR7.
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Affiliation(s)
- Lisa Mathiasen
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | | | - Angela Cattaneo
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Francesco Blasi
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
| | | | - Chiara Bruckmann
- FIRC (Foundation for Italian Cancer Research) Institute of Molecular Oncology (IFOM), Milan, Italy
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7
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Association of GABRA6 1519 T>C (rs3219151) and Synapsin II (rs37733634) gene polymorphisms with the development of idiopathic generalized epilepsy. Epilepsy Res 2014; 108:1267-73. [DOI: 10.1016/j.eplepsyres.2014.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 06/18/2014] [Accepted: 07/09/2014] [Indexed: 11/22/2022]
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8
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Pelassa I, Corà D, Cesano F, Monje FJ, Montarolo PG, Fiumara F. Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction. Hum Mol Genet 2014; 23:3402-20. [PMID: 24497578 PMCID: PMC4049302 DOI: 10.1093/hmg/ddu049] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The expansion of homopolymeric glutamine (polyQ) or alanine (polyA) repeats in certain proteins owing to genetic mutations induces protein aggregation and toxicity, causing at least 18 human diseases. PolyQ and polyA repeats can also associate in the same proteins, but the general extent of their association in proteomes is unknown. Furthermore, the structural mechanisms by which their expansion causes disease are not well understood, and these repeats are generally thought to misfold upon expansion into aggregation-prone β-sheet structures like amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) structures in triggering aggregation and toxicity of polyQ-expanded proteins, raising the possibility that polyA repeats may as well form these structures, by themselves or in association with polyQ. We found through bioinformatics screenings that polyA, polyQ and polyQA repeats have a phylogenetically graded association in human and non-human proteomes and associate/overlap with CC domains. Circular dichroism and cross-linking experiments revealed that polyA repeats can form—alone or with polyQ and polyQA—CC structures that increase in stability with polyA length, forming higher-order multimers and polymers in vitro. Using structure-guided mutagenesis, we studied the relevance of polyA CCs to the in vivo aggregation and toxicity of RUNX2—a polyQ/polyA protein associated with cleidocranial dysplasia upon polyA expansion—and found that the stability of its polyQ/polyA CC controls its aggregation, localization and toxicity. These findings indicate that, like polyQ, polyA repeats form CC structures that can trigger protein aggregation and toxicity upon expansion in human genetic diseases.
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Affiliation(s)
| | - Davide Corà
- Center for Molecular Systems Biology, University of Torino, Torino 10123, Italy
| | - Federico Cesano
- Department of Chemistry, University of Torino, Torino 10125, Italy
| | - Francisco J. Monje
- Department of Neurophysiology and Neuropharmacology,Medical University of Vienna, Vienna 1090, Austria
| | - Pier Giorgio Montarolo
- Department of Neuroscience and
- National Institute of Neuroscience (INN), Torino 10125, Italy
| | - Ferdinando Fiumara
- Department of Neuroscience and
- To whom correspondence should be addressed at: Department of Neuroscience, University of Torino, Corso Raffaello 30, Torino 10125, Italy. Tel: +39-0116708486;
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Kumar A, Bhandari A, Sarde SJ, Goswami C. Genetic variants and evolutionary analyses of heparin cofactor II. Immunobiology 2014; 219:713-28. [PMID: 24950623 DOI: 10.1016/j.imbio.2014.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/13/2014] [Accepted: 05/19/2014] [Indexed: 11/25/2022]
Abstract
Heparin cofactor II (HCII) belongs to serpin superfamily and it acts as a thrombin inhibitor in the coagulation cascade, in a glycosaminoglycan-dependent pathway using the release of a sequestered hirudin-like N-terminal tail for interaction with thrombin. This serpin belongs to multiple member group V2 of vertebrate serpin classification. However, there is no comprehensive study illustrating the exact phylogenetic history of HCII, to date. Herein, we explored phylogenetic traits of HCII genes. Structures of HCII gene from selected ray-finned fishes and lamprey varied in exon I and II with insertions of novel introns of which one in core domain for ray-finned fishes in exon II at the position 241c. We found HCII remain nested in the largest intron of phosphatidylinositol (PI) 4-kinase (PIK4CA) gene (genetic variants of this gene cause schizophrenia) at the origin of vertebrates, dated about 500MY old. We found that sequence features such as two acidic repeats (AR1-II), GAG-binding helix-D, three serpin motifs and inhibitory reactive center loop (RCL) of HCII protein are highly conserved in 55 vertebrates analyzed. We identified 985 HCII variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (84.3%), insertion (7.1%) and deletion (5.0%). We identified 37 deleterious mutations in the human HCII protein and we have described these mutations in relation to HCII sequence-structure-function relationships. These understandings may have clinical and medical importance as well.
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Affiliation(s)
- Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany.
| | - Anita Bhandari
- Molecular Physiology, Zoological Institute, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Sandeep J Sarde
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany; Master Program Agrigenomics, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Chandan Goswami
- National Institute of Science Education and Research, Bhubaneswar, Orissa, India
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10
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Waldeck W, Mueller G, Glatting KH, Hotz-Wagenblatt A, Diessl N, Chotewutmonti S, Langowski J, Semmler W, Wiessler M, Braun K. Spatial localization of genes determined by intranuclear DNA fragmentation with the fusion proteins lamin KRED and histone KRED und visible light. Int J Med Sci 2013; 10:1136-48. [PMID: 23869190 PMCID: PMC3714390 DOI: 10.7150/ijms.6121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 06/06/2013] [Indexed: 12/02/2022] Open
Abstract
The highly organized DNA architecture inside of the nuclei of cells is accepted in the scientific world. In the human genome about 3 billion nucleotides are organized as chromatin in the cell nucleus. In general, they are involved in gene regulation and transcription by histone modification. Small chromosomes are localized in a central nuclear position whereas the large chromosomes are peripherally positioned. In our experiments we inserted fusion proteins consisting of a component of the nuclear lamina (lamin B1) and also histone H2A, both combined with the light inducible fluorescence protein KillerRed (KRED). After activation, KRED generates reactive oxygen species (ROS) producing toxic effects and may cause cell death. We analyzed the spatial damage distribution in the chromatin after illumination of the cells with visible light. The extent of DNA damage was strongly dependent on its localization inside of nuclei. The ROS activity allowed to gain information about the location of genes and their functions via sequencing and data base analysis of the double strand breaks of the isolated DNA. A connection between the damaged gene sequences and some diseases was found.
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Affiliation(s)
- Waldemar Waldeck
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Gabriele Mueller
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Karl-Heinz Glatting
- 3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- 3. German Cancer Research Center, Genomics Proteomics Core Facility HUSAR Bioinformatics Lab, INF 580, D-69120 Heidelberg, Germany
| | - Nicolle Diessl
- 4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany
| | - Sasithorn Chotewutmonti
- 4. German Cancer Research Center, Genomics and Proteomics Core Facility High Throughput Sequencing, INF 580, D-69120 Heidelberg, Germany
| | - Jörg Langowski
- 1. German Cancer Research Center, Dept. of Biophysics of Macromolecules, INF 580, D-69120 Heidelberg, Germany
| | - Wolfhard Semmler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Manfred Wiessler
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
| | - Klaus Braun
- 2. German Cancer Research Center, Dept. of Medical Physics in Radiology, INF 280, D-69120 Heidelberg, Germany
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11
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Behura SK, Severson DW. Overlapping genes of Aedes aegypti: evolutionary implications from comparison with orthologs of Anopheles gambiae and other insects. BMC Evol Biol 2013; 13:124. [PMID: 23777277 PMCID: PMC3689595 DOI: 10.1186/1471-2148-13-124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 06/12/2013] [Indexed: 11/11/2022] Open
Abstract
Background Although gene overlapping is a common feature of prokaryote and mitochondria genomes, such genes have also been identified in many eukaryotes. The overlapping genes in eukaryotes are extensively rearranged even between closely related species. In this study, we investigated retention and rearrangement of positionally overlapping genes between the mosquitoes Aedes aegypti (dengue virus vector) and Anopheles gambiae (malaria vector). The overlapping gene pairs of A. aegypti were further compared with orthologs of other selected insects to conduct several hypothesis driven investigations relating to the evolution and rearrangement of overlapping genes. Results The results show that as much as ~10% of the predicted genes of A. aegypti and A. gambiae are localized in positional overlapping manner. Furthermore, the study shows that differential abundance of introns and simple sequence repeats have significant association with positional rearrangement of overlapping genes between the two species. Gene expression analysis further suggests that antisense transcripts generated from the oppositely oriented overlapping genes are differentially regulated and may have important regulatory functions in these mosquitoes. Our data further shows that synonymous and non-synonymous mutations have differential but non-significant effect on overlapping localization of orthologous genes in other insect genomes. Conclusion Gene overlapping in insects may be a species-specific evolutionary process as evident from non-dependency of gene overlapping with species phylogeny. Based on the results, our study suggests that overlapping genes may have played an important role in genome evolution of insects.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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12
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Hughes JN, Thomas PQ. Molecular pathology of polyalanine expansion disorders: new perspectives from mouse models. Methods Mol Biol 2013; 1017:135-51. [PMID: 23719913 DOI: 10.1007/978-1-62703-438-8_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Disease-causing polyalanine (PA) expansion mutations have been identified in nine genes, eight of which encode transcription factors (TFs) with important roles in development. In vitro and cell overexpression studies have shown that expanded PA tracts result in protein misfolding and the formation of aggregates. This feature of PA proteins is reminiscent of the related polyglutamine (PQ) disease proteins, which have been shown to cause disease via a gain-of-function (GOF) mechanism. However, in sharp contrast to PQ disorders, the disease phenotypes associated with PA mutations are more consistent with a LOF and/or mild GOF mechanism, suggesting that their molecular pathology is inherently different to PQ disorders. Elucidating the cellular impact of PA mutations in vivo has been difficult to address as, unlike the late-onset polyglutamine disorders, all PA disorders associated with TF gene mutations are congenital. However, in recent years, significant advances have been made through the analysis of engineered (knock-in) and spontaneous PA mouse models. Here we review these recent findings and propose an updated model of the molecular and cellular mechanism of PA disorders that incorporates both LOF and GOF features.
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Affiliation(s)
- James N Hughes
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
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13
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Jorda J, Kajava AV. Protein homorepeats sequences, structures, evolution, and functions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 79:59-88. [PMID: 20621281 DOI: 10.1016/s1876-1623(10)79002-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The vast majority of protein sequences are aperiodic; they do not have any strong bias in the amino acid composition, and they use a subtle mixture of all or most of the 20 amino acid residues to code a great number of various structures and functions. In this context, homorepeats, runs of a single amino acid residue, represent unusual, eye-catching motifs in proteins. Despite the sequence simplicity and relatively small size, the homorepeat runs have a strong potential for molecular interactions due to the excessively high local concentration of a certain physico-chemical property. Appearance of such runs within proteins may give them new structural and functional features. An increasing number of studies demonstrate the abundance of these motifs in proteins, their important roles in biological processes, and their link to a number of hereditary and age-related diseases. In this chapter, we summarize data on the distribution of homorepeats in proteomes and on their structural properties, evolution, and functions.
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Affiliation(s)
- Julien Jorda
- Centre de Recherches de Biochimie Macromoléculaire UMR 5237, CNRS, University of Montpellier 1 and 2, Montpellier, France
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14
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A novel protein, sperm head and tail associated protein (SHTAP), interacts with cysteine-rich secretory protein 2 (CRISP2) during spermatogenesis in the mouse. Biol Cell 2009; 102:93-106. [PMID: 19686095 DOI: 10.1042/bc20090099] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION CRISP2 (cysteine-rich secretory protein 2) is a sperm acrosome and tail protein with the ability to regulate Ca2+ flow through ryanodine receptors. Based on these properties, CRISP2 has a potential role in fertilization through the regulation of ion signalling in the acrosome reaction and sperm motility. The purpose of the present study was to determine the expression, subcellular localization and the role in spermatogenesis of a novel CRISP2-binding partner, which we have designated SHTAP (sperm head and tail associated protein). RESULTS Using yeast two-hybrid screens of an adult testis expression library, we identified SHTAP as a novel mouse CRISP2-binding partner. Sequence analysis of all Shtap cDNA clones revealed that the mouse Shtap gene is embedded within a gene encoding the unrelated protein NSUN4 (NOL1/NOP2/Sun domain family member 4). Five orthologues of the Shtap gene have been annotated in public databases. SHTAP and its orthologues showed no significant sequence similarity to any known protein or functional motifs, including NSUN4. Using an SHTAP antiserum, multiple SHTAP isoforms (approximately 20-87 kDa) were detected in the testis, sperm, and various somatic tissues. Interestingly, only the approximately 26 kDa isoform of SHTAP was able to interact with CRISP2. Furthermore, yeast two-hybrid assays showed that both the CAP (CRISP/antigen 5/pathogenesis related-1) and CRISP domains of CRISP2 were required for maximal binding to SHTAP. SHTAP protein was localized to the peri-acrosomal region of round spermatids, and the head and tail of the elongated spermatids and sperm tail where it co-localized with CRISP2. During sperm capacitation, SHTAP and the SHTAP-CRISP2 complex appeared to be redistributed within the head. CONCLUSIONS The present study is the first report of the identification, annotation and expression analysis of the mouse Shtap gene. The redistribution observed during sperm capacitation raises the possibility that SHTAP and the SHTAP-CRISP2 complex play a role in the attainment of sperm functional competence.
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15
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Wang Y, Yu L, Zhao T, Xu J, Liu Z, Liu Y, Feng G, He L, Li S. No association between bipolar disorder and syngr1 or synapsin II polymorphisms in the Han Chinese population. Psychiatry Res 2009; 169:167-8. [PMID: 19665806 DOI: 10.1016/j.psychres.2008.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Revised: 10/30/2008] [Accepted: 12/22/2008] [Indexed: 11/30/2022]
Abstract
Polymorphisms of the SYNAPTOGYRIN1 (SYNGR1) and SYNASINII (SYNII) genes have been shown to be a risk factor for bipolar disorder or schizophrenia. A case-control study with these two genes was conducted in 506 bipolar disorder patients and 507 healthy individuals from the Han Chinese population. No association was found in this study.
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Affiliation(s)
- Yabing Wang
- Institute for Nutritional Sciences, SIBS, Chinese Academy of Sciences, Shanghai 200031, PR China; Bio-X Center, Shanghai Jiao Tong University, Shanghai 200030, PR China
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16
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17
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Lin MF, Deoras AN, Rasmussen MD, Kellis M. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol 2008; 4:e1000067. [PMID: 18421375 PMCID: PMC2291194 DOI: 10.1371/journal.pcbi.1000067] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 03/20/2008] [Indexed: 01/22/2023] Open
Abstract
Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (< or =240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human.
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Affiliation(s)
- Michael F. Lin
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Ameya N. Deoras
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Matthew D. Rasmussen
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Manolis Kellis
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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18
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Oma Y, Kino Y, Toriumi K, Sasagawa N, Ishiura S. Interactions between homopolymeric amino acids (HPAAs). Protein Sci 2007; 16:2195-204. [PMID: 17766374 PMCID: PMC2204140 DOI: 10.1110/ps.072955307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Many human proteins contain consecutive amino acid repeats, known as homopolymeric amino acid (HPAA) tracts. Some inherited diseases are caused by proteins in which HPAAs are expanded to an excessive length. To this day, nine polyglutamine-related diseases and nine polyalanine-related diseases have been reported, including Huntington's disease and oculopharyngeal muscular dystrophy. In this study, potential HPAA-HPAA interactions were examined by yeast two-hybrid assays using HPAAs of approximately 30 residues in length. The results indicate that hydrophobic HPAAs interact with themselves and with other hydrophobic HPAAs. Previously, we reported that hydrophobic HPAAs formed large aggregates in COS-7 cells. Here, those HPAAs were shown to have significant interactions with each other, suggesting that hydrophobicity plays an important role in aggregation. Among the observed HPAA-HPAA interactions, the Ala28-Ala29 interaction was notable because polyalanine tracts of these lengths have been established to be pathogenic in several polyalanine-related diseases. By testing several constructs of different lengths, we clarified that polyalanine self-interacts at longer lengths (>23 residues) but not at shorter lengths (six to approximately 23 residues) in a yeast two-hybrid assay and a GST pulldown assay. This self-interaction was found to be SDS sensitive in SDS-PAGE and native-PAGE assays. Moreover, the intracellular localization of these long polyalanine tracts was also observed to be disturbed. Our results suggest that long tracts of polyalanine acquire SDS-sensitive self-association properties, which may be a prerequisite event for their abnormal folding. The misfolding of these tracts is thought to be a common molecular aspect underlying the pathogenesis of polyalanine-related diseases.
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Affiliation(s)
- Yoko Oma
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
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19
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Abu-Baker A, Rouleau GA. Oculopharyngeal muscular dystrophy: Recent advances in the understanding of the molecular pathogenic mechanisms and treatment strategies. Biochim Biophys Acta Mol Basis Dis 2007; 1772:173-85. [PMID: 17110089 DOI: 10.1016/j.bbadis.2006.10.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2006] [Revised: 10/05/2006] [Accepted: 10/06/2006] [Indexed: 12/24/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. OPMD is caused by a small expansion of a short polyalanine tract in the poly (A) binding protein nuclear 1 protein (PABPN1). The mechanism by which the polyalanine expansion mutation in PABPN1 causes disease is unclear. PABPN1 is a nuclear multi-functional protein which is involved in pre-mRNA polyadenylation, transcription regulation, and mRNA nucleocytoplasmic transport. The distinct pathological hallmark of OPMD is the presence of filamentous intranuclear inclusions (INIs) in patient's skeletal muscle cells. The exact relationship between mutant PABPN1 intranuclear aggregates and pathology is not clear. OPMD is a unique disease sharing common pathogenic features with other polyalanine disorders, as well as with polyglutamine and dystrophic disorders. This chapter aims to review the rapidly growing body of knowledge concerning OPMD. First, we outline the background of OPMD. Second, we compare OPMD with other trinucleotide repeat disorders. Third, we discuss the recent advances in the understanding of the molecular mechanisms underlying OPMD pathogenesis. Finally, we review recent therapeutic strategies for OPMD.
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Affiliation(s)
- Aida Abu-Baker
- Center for the Study of Brain Diseases, CHUM Research Center-Notre Dame Hospital, J.A. de Sève Pavillion, Room Y-3633, 1560, Sherbrooke Street East, Montreal, QC, Canada H2L 4M1
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20
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Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila. BMC Evol Biol 2006; 6:106. [PMID: 17163987 PMCID: PMC1764764 DOI: 10.1186/1471-2148-6-106] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 12/12/2006] [Indexed: 12/02/2022] Open
Abstract
Background It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it. Results We have measured the rates of nucleotide divergence and indel fixation of three Hox genes, labial (lab), proboscipedia (pb) and abdominal-A (abd-A), and compared them with those of three genes derived by duplication from Hox3, bicoid (bcd), zerknüllt (zen) and zerknüllt-related (zen2), and 15 non-Hox genes in sets of orthologous sequences of three species of the genus Drosophila. These rates were compared to test the hypothesis that Hox genes evolve slowly. Our results show that the evolutionary rate of Hox genes is higher than that of non-Hox genes when both amino acid differences and indels are taken into account: 43.39% of the amino acid sequence is altered in Hox genes, versus 30.97% in non-Hox genes and 64.73% in Hox-derived genes. Microsatellites scattered along the coding sequence of Hox genes explain partially, but not fully, their fast sequence evolution. Conclusion These results show that Hox genes have a higher evolutionary dynamics than other developmental genes, and emphasize the need to take into account indels in addition to nucleotide substitutions in order to accurately estimate evolutionary rates.
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21
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Piehler AP, Wenzel JJ, Olstad OK, Haug KBF, Kierulf P, Kaminski WE. The human ortholog of the rodent testis-specific ABC transporter Abca17 is a ubiquitously expressed pseudogene (ABCA17P) and shares a common 5' end with ABCA3. BMC Mol Biol 2006; 7:28. [PMID: 16968533 PMCID: PMC1579226 DOI: 10.1186/1471-2199-7-28] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 09/12/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the past years, we and others discovered a series of human ATP-binding cassette (ABC) transporters, now referred to as ABC A-subfamily transporters. Recently, a novel testis-specific ABC A transporter, Abca17, has been cloned in rodent. In this study, we report the identification and characterization of the human ortholog of rodent Abca17. RESULTS The novel human ABC A-transporter gene on chromosome 16p13.3 is ubiquitously expressed with highest expression in glandular tissues and the heart. The new ABC transporter gene exhibits striking nucleotide sequence homology with the recently cloned mouse (58%) and rat Abca17 (51%), respectively, and is located in the syntenic region of mouse Abca17 indicating that it represents the human ortholog of rodent Abca17. However, unlike in the mouse, the full-length ABCA17 transcript (4.3 kb) contains numerous mutations that preclude its translation into a bona fide ABC transporter protein strongly suggesting that the human ABCA17 gene is a transcribed pseudogene (ABCA17P). We identified numerous alternative ABCA17P splice variants which are transcribed from two distinct transcription initiation sites. Genomic analysis revealed that ABCA17P borders on another ABC A-subfamily transporter - the lung surfactant deficiency gene ABCA3. Surprisingly, we found that both genes overlap at their first exons and are transcribed from opposite strands. This genomic colocalization and the observation that the ABCA17P and ABCA3 genes share significant homologies in several exons (up to 98%) suggest that both genes have evolved by gene duplication. CONCLUSION Our results demonstrate that ABCA17P and ABCA3 form a complex of overlapping genes in the human genome from which both non-coding and protein-coding ABC A-transporter RNAs are expressed. The fact that both genes overlap at their 5' ends suggests interdependencies in their regulation and may have important implications for the functional analysis of the disease gene ABCA3. Moreover, this is the first demonstration of the expression of a pseudogene and its parent gene from a common overlapping DNA region in the human genome.
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Affiliation(s)
- Armin P Piehler
- R&D Group, Department of Clinical Chemistry, Ulleval University Hospital, 0407 Oslo, Norway
| | - Jürgen J Wenzel
- Department of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Hospital, 55101 Mainz, Germany
| | - Ole K Olstad
- R&D Group, Department of Clinical Chemistry, Ulleval University Hospital, 0407 Oslo, Norway
| | - Kari Bente Foss Haug
- R&D Group, Department of Clinical Chemistry, Ulleval University Hospital, 0407 Oslo, Norway
| | - Peter Kierulf
- R&D Group, Department of Clinical Chemistry, Ulleval University Hospital, 0407 Oslo, Norway
| | - Wolfgang E Kaminski
- Institute for Clinical Chemistry, University of Heidelberg, 68167 Mannheim, Germany
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22
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Veith AM, Schäfer M, Klüver N, Schmidt C, Schultheis C, Schartl M, Winkler C, Volff JN. Tissue-Specific Expression ofdmrtGenes in Embryos and Adults of the PlatyfishXiphophorus maculatus. Zebrafish 2006; 3:325-37. [DOI: 10.1089/zeb.2006.3.325] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Anne-Marie Veith
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Matthias Schäfer
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Nils Klüver
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Cornelia Schmidt
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | | | - Manfred Schartl
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Christoph Winkler
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Jean-Nicolas Volff
- Physiologische Chemie I, Biozentrum, University of Würzburg, Würzburg, Germany
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23
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Uhlenhaut NH, Treier M. Foxl2 function in ovarian development. Mol Genet Metab 2006; 88:225-34. [PMID: 16647286 DOI: 10.1016/j.ymgme.2006.03.005] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Revised: 03/09/2006] [Accepted: 03/09/2006] [Indexed: 01/12/2023]
Abstract
Foxl2 is a forkhead transcription factor essential for proper reproductive function in females. Human patients carrying mutations in the FOXL2 gene display blepharophimosis/ptosis/epicanthus inversus syndrome (BPES), an autosomal dominant disease associated with eyelid defects and premature ovarian failure in females. Recently, animal models for BPES have been developed that in combination with a catalogue of human FOXL2 mutations provide further insight into its molecular function. Mice homozygous mutant for Foxl2 display craniofacial malformations and female infertility. The analysis of the murine phenotype has revealed that Foxl2 is required for granulosa cell function. These ovarian somatic cells surround and nourish the oocyte and play an important role in follicle formation and activation. Mutations upstream of FOXL2 in humans, not affecting the coding sequence itself, have also been shown to cause BPES, which points to the existence of a distant regulatory element necessary for proper gene expression. The same regulatory sequences may be deleted in the goat polled intersex syndrome (PIS), in which FoxL2 expression is severely reduced. Sequence comparison of FoxL2 from several vertebrate species has shown that it is a highly conserved gene involved in ovary development. Thus, the detailed understanding of Foxl2 function and regulation and the identification of its transcriptional targets may open new avenues for the treatment of female infertility in the future.
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Affiliation(s)
- Nina Henriette Uhlenhaut
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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24
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Hodgson U, Pulkkinen V, Dixon M, Peyrard-Janvid M, Rehn M, Lahermo P, Ollikainen V, Salmenkivi K, Kinnula V, Kere J, Tukiainen P, Laitinen T. ELMOD2 is a candidate gene for familial idiopathic pulmonary fibrosis. Am J Hum Genet 2006; 79:149-54. [PMID: 16773575 PMCID: PMC1474126 DOI: 10.1086/504639] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 03/27/2006] [Indexed: 11/04/2022] Open
Abstract
We performed a genomewide scan in six multiplex families with familial idiopathic pulmonary fibrosis (IPF) who originated from southeastern Finland. The majority of the Finnish multiplex families were clustered in the region, and the population history suggested that the clustering might be explained by an ancestor shared among the patients. The genomewide scan identified five loci of interest. The hierarchical fine mapping in an extended data set with 24 families originating from the same geographic region revealed a shared 110 kb to 13 Mb haplotype on chromosome 4q31, which was significantly more frequent among the patients than in population-based controls (odds ratio 6.3; 95% CI 2.5-15.9; P = .0001). The shared haplotype harbored two functionally uncharacterized genes, ELMOD2 and LOC152586, of which only ELMOD2 was expressed in lung and showed significantly decreased messenger-RNA expression in IPF lung (n = 6) when compared with that of healthy lung (n = 7; P = .05). Our results suggest ELMOD2 as a novel candidate gene for susceptibility in familial IPF.
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Affiliation(s)
- Ulla Hodgson
- Department of Pulmonary Medicine, Helsinki University Central Hospital, Finland.
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25
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Tufarelli C. The silence RNA keeps: cis mechanisms of RNA mediated epigenetic silencing in mammals. Philos Trans R Soc Lond B Biol Sci 2006; 361:67-79. [PMID: 16553309 PMCID: PMC1626536 DOI: 10.1098/rstb.2005.1732] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the fundamental questions of modern biology is to unravel how genes are switched on and off at the right time and in the correct tissues. It is well recognized that gene regulation depends on a dynamic balance between activating and repressing forces, and multiple mechanisms are involved in both gene silencing and activation. Work over the last decade has revealed that in some cases transcriptional silencing of specific genes is mediated by RNAs that specifically recruit repressing complexes to homologous DNA sequences. Examples of both cis and trans RNA driven transcriptional silencing have been reported. This review focuses on those examples of transcriptional gene silencing in which the RNA component seems to act uniquely in cis. Speculative models of how such cis acting transcripts may trigger transcriptional silencing are proposed. Future experimental testing of these and other mechanisms is important to gain a fuller understanding of how genes are regulated and to identify instances in which such mechanisms are defective, leading to disease. Understanding the basic molecular basis of these phenomena will provide us with invaluable tools for the future development of targeted therapies and drugs for those diseases in which they are faulty.
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Affiliation(s)
- Cristina Tufarelli
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
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26
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Yu P, Ma D, Xu M. Nested genes in the human genome. Genomics 2006; 86:414-22. [PMID: 16084061 DOI: 10.1016/j.ygeno.2005.06.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 06/05/2005] [Accepted: 06/15/2005] [Indexed: 12/01/2022]
Abstract
Here we studied one special type of gene, i.e., the nested gene, in the human genome. We collected 373 reliably annotated nested genes. Two-thirds of them were on the strand opposite that of their host gene. About 58% coding nested gene pairs were conserved in mouse and some were even maintained in chicken and fish, while nested pseudogenes were poorly conserved. Ka/Ks analysis revealed that nested genes were under strong selection, although they did not demonstrate greater conservation than other genes. With microarray data we observed that two partners of one nested pair seemed to be expressed reciprocally. A significant proportion of nested genes were tissue-specifically expressed. Gene ontology analysis demonstrated that quite a number of nested genes participated in cellular signal transduction. Based on these observations, we think that nested genes are a group of genes with important physiological functions.
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Affiliation(s)
- Peng Yu
- Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University, Beijing 100083, People's Republic of China.
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Trochet D, Hong SJ, Lim JK, Brunet JF, Munnich A, Kim KS, Lyonnet S, Goridis C, Amiel J. Molecular consequences of PHOX2B missense, frameshift and alanine expansion mutations leading to autonomic dysfunction. Hum Mol Genet 2005; 14:3697-708. [PMID: 16249188 DOI: 10.1093/hmg/ddi401] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Heterozygous mutations of the PHOX2B gene account for a broad variety of disorders of the autonomic nervous system, either isolated or combined, including congenital central hypoventilation syndrome (CCHS), tumours of the sympathetic nervous system and Hirschsprung disease. In CCHS, the prevalent mutation is an expansion of a 20-alanine stretch ranging from +5 to +13 alanines, whereas frameshift and missense mutations are found occasionally. To determine the molecular basis of impaired PHOX2B function, we assayed the transactivation and DNA binding properties of wild-type and mutant PHOX2B proteins. Furthermore, we investigated aggregate formation by proteins with polyalanine tract expansions ranging from +5 to +13 alanines using immunofluorescence of transfected cells and gel filtration of in vitro translated proteins. We found that transactivation of the dopamine beta-hydroxylase promoter by PHOX2B proteins with frameshift and missense mutations was abolished or severely curtailed, as was in vitro DNA binding although the proteins localized to the nucleus. The transactivation potential of proteins with polyalanine tract expansions declined with increasing length of the polyalanine stretch, and DNA binding was affected for an expansion of +9 alanines and above. Cytoplasmic aggregation in transfected cells was only observed for the longest expansions, whereas even the short expansion mutants were prone to form multimers in vitro. Such a tendency to protein misfolding could explain loss of transactivation for alanine expansion mutations. However, additional mechanisms such as toxic gain-of-function may play a role in the pathogenic process.
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Affiliation(s)
- Delphine Trochet
- Université Paris-Descartes, Faculté de Médecine; INSERM; AP-HP, Hôpital Necker-Enfants Malades, INSERM U-393, Paris, France
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Lee HJ, Song JY, Kim JW, Jin SY, Hong MS, Park JK, Chung JH, Shibata H, Fukumaki Y. Association study of polymorphisms in synaptic vesicle-associated genes, SYN2 and CPLX2, with schizophrenia. Behav Brain Funct 2005; 1:15. [PMID: 16131404 PMCID: PMC1215472 DOI: 10.1186/1744-9081-1-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 08/31/2005] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The occurrence of aberrant functional connectivity in the neuronal circuit is one of the integrative theories of the etiology of schizophrenia. Previous studies have reported that the protein and mRNA levels of the synapsin 2 (SYN2) and complexin 2 (CPLX2) genes were decreased in patients with schizophrenia. Synapsin 2 and complexin 2 are involved in synaptogenesis and the modulation of neurotransmitter release. This report presents a study of the association of polymorphisms of SYN2 and CPLX2 with schizophrenia in the Korean population. METHODS Six single nucleotide polymorphisms (SNPs) and one 5-bp insertion/deletion in SYN2 and five SNPs in CPLX2 were genotyped in 154 Korean patients with schizophrenia and 133 control patients using direct sequencing or restriction fragment length polymorphism analysis. An intermarker linkage disequilibrium map was constructed for each gene. RESULTS Although there was no significant difference in the genotypic distributions and allelic frequencies of either SYN2 or CPLX2 polymorphisms between the schizophrenia and control groups, the two-way haplotype analyses revealed significant associations with the disease (P < 0.05 after Bonferroni correction). The three-way haplotype analyses also revealed a significant association of SYN2 with schizophrenia (P < 0.001 after Bonferroni correction). CONCLUSION These results suggest that both SYN2 and CPLX2 may confer susceptibility to schizophrenia in the Korean population.
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Affiliation(s)
- Hee Jae Lee
- Medical Science Institute, Kangwon National University, Chunchon, Republic of Korea
- Division of Disease Genes, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ji Young Song
- Department of Neuropsychiatry, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jong Woo Kim
- Department of Neuropsychiatry, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Sheng-Yu Jin
- Kohwang Medical Research Institute, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Mi Suk Hong
- Kohwang Medical Research Institute, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jin Kyoung Park
- Department of Neuropsychiatry, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Joo-Ho Chung
- Kohwang Medical Research Institute, College of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hiroki Shibata
- Division of Disease Genes, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Fukumaki
- Division of Disease Genes, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Hamady M, Cheung THT, Resing K, Cios KJ, Knight R. Key challenges in proteomics and proteoinformatics. Progress in proteins. ACTA ACUST UNITED AC 2005; 24:34-40. [PMID: 15971839 DOI: 10.1109/memb.2005.1436456] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Micah Hamady
- Department of Computer Science, University of Colorado at Boulder, USA
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Makalowska I, Lin CF, Makalowski W. Overlapping genes in vertebrate genomes. Comput Biol Chem 2005; 29:1-12. [PMID: 15680581 DOI: 10.1016/j.compbiolchem.2004.12.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 12/15/2004] [Accepted: 12/15/2004] [Indexed: 11/19/2022]
Abstract
Overlapping genes in mammalian genomes are unexpected phenomena even though hundreds of pairs of protein coding overlapping genes have been reported so far. Overlapping genes can be divided into different categories based on direction of transcription as well as on sequence segments being shared between overlapping coding regions. The biologic functions of natural antisense transcripts, their involvement in physiological processes and gene regulation in living organisms are not fully understood. Number of documented examples indicates that they may exert control at various levels of gene expression, such as transcription, mRNA processing, splicing, stability, transport, and translation. Similarly, evolutionary origin of such genes is not known, existing hypotheses can explain only selected cases of mammalian gene overlaps which could originate as result of rearrangements, overprinting and/or adoption of signals in the neighboring gene locus.
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Affiliation(s)
- Izabela Makalowska
- The Huck Institute of the Life Sciences, The Pennsylvania State University, 502 Wartik Lab, University Park, PA 16802, USA.
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Singh GP, Chandra BR, Bhattacharya A, Akhouri RR, Singh SK, Sharma A. Hyper-expansion of asparagines correlates with an abundance of proteins with prion-like domains in Plasmodium falciparum. Mol Biochem Parasitol 2005; 137:307-19. [PMID: 15383301 DOI: 10.1016/j.molbiopara.2004.05.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Revised: 05/04/2004] [Accepted: 05/14/2004] [Indexed: 11/20/2022]
Abstract
Plasmodium falciparum encodes approximately 5300 proteins of which approximately 35% have repeats of amino acids, significantly higher than in other fully sequenced eukaryotes. The proportion of proteins with amino acid homorepeats varies from 4 to 54% amongst different functional classes of proteins. These homorepeats are dominated by asparagines, which are selected over lysines despite equivalent AT codon content. Surprisingly, asparagine repeats are absent from the variant surface antigen protein families of PfEMP1s, Stevors and Rifins. The PfEMP1 protein family is instead rich in recurrences of glutamates, similar to human cell surface proteins. Structural mapping of homorepeats suggests that these segments are likely to form surface exposed structures that protrude from the main protein cores. We also found an abundance of asparagine-rich prion-like domains in P. falciparum, significantly larger than in any other eukaryote. Domains rich in glutamines and asparagines have an innate predisposition to form self-propagating amyloid fibers, which are involved both in prion-based inheritance and in human neurodegenerative disorders. Nearly 24% (1302 polypeptides) of P. falciparum proteins contain prion-forming or prion-inducing domains, in comparison to Drosophila (approximately 3.4%) which to date showed the highest number of prion-like proteins. The unexpected properties of P. falciparum revealed here open new avenues for investigating parasite biology.
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Affiliation(s)
- Gajinder Pal Singh
- Malaria Research Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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Adie EA, Adams RR, Evans KL, Porteous DJ, Pickard BS. Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics 2005; 6:55. [PMID: 15766383 PMCID: PMC1274252 DOI: 10.1186/1471-2105-6-55] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Accepted: 03/14/2005] [Indexed: 11/26/2022] Open
Abstract
Background Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation to knowledge of the disease or phenotype in question. However, here we show that disease genes share patterns of sequence-based features that can provide a good basis for automatic prioritization of candidates by machine learning. Results We examined a variety of sequence-based features and found that for many of them there are significant differences between the sets of genes known to be involved in human hereditary disease and those not known to be involved in disease. We have created an automatic classifier called PROSPECTR based on those features using the alternating decision tree algorithm which ranks genes in the order of likelihood of involvement in disease. On average, PROSPECTR enriches lists for disease genes two-fold 77% of the time, five-fold 37% of the time and twenty-fold 11% of the time. Conclusion PROSPECTR is a simple and effective way to identify genes involved in Mendelian and oligogenic disorders. It performs markedly better than the single existing sequence-based classifier on novel data. PROSPECTR could save investigators looking at large regions of interest time and effort by prioritizing positional candidate genes for mutation detection and case-control association studies.
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Affiliation(s)
- Euan A Adie
- Medical Genetics Section, Department of Medical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Richard R Adams
- Medical Genetics Section, Department of Medical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Medical Genetics Section, Department of Medical Sciences, The University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Medical Genetics Section, Department of Medical Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ben S Pickard
- Medical Genetics Section, Department of Medical Sciences, The University of Edinburgh, Edinburgh, UK
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Chen Q, He G, Qin W, Chen QY, Zhao XZ, Duan SW, Liu XM, Feng GY, Xu YF, St Clair D, Li M, Wang JH, Xing YL, Shi JG, He L. Family-based association study of synapsin II and schizophrenia. Am J Hum Genet 2004; 75:873-7. [PMID: 15449241 PMCID: PMC1182116 DOI: 10.1086/425588] [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] [Received: 06/28/2004] [Accepted: 09/02/2004] [Indexed: 01/11/2023] Open
Abstract
Synapsin II has been proposed as a candidate gene for vulnerability to schizophrenia on the basis of its function and its location in a region of the genome implicated by linkage studies in families with schizophrenia. We recently reported positive association of synapsin II with schizophrenia in a case-control study (Chen et al. 2004). However, since case-control analyses can generate false-positive results in the presence of minor degrees of population stratification, we have performed a replication study in 366 additional Han Chinese probands and their parents by use of analyses of transmission/disequilibrium for three in/del markers and three single-nucleotide polymorphisms. Positive association was observed for rs2307981 (P =.02), rs2308169 (P =.005), rs308963 (P =.002), rs795009 (P =.02), and rs2307973 (P =.02). For transmission of six-marker haplotypes, the global P value was.0000016 (5 degrees of freedom), principally because of overtransmission of the most common haplotype, CAA/-/G/T/C/- (frequency 53.6%; chi (2) = 20.8; P =.0000051). This confirms our previous study and provides further support for the role of synapsin II variants in susceptibility to schizophrenia.
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Affiliation(s)
- Qi Chen
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Guang He
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Wei Qin
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Qing-ying Chen
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Xin-zhi Zhao
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Shi-wei Duan
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Xin-min Liu
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Guo-yin Feng
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Yi-feng Xu
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - David St Clair
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Min Li
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Jin-huan Wang
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Yang-ling Xing
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Jian-guo Shi
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Lin He
- Neuropsychiatric and Human Genetics Group, Bio-X Life Science Research Center, Shanghai Jiao Tong University, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Institute of Mental Health, Shanghai; Department of Pathophysiology, Medical School of Soochow University, Suzhou, China; Liaoning Institute of Mental Health, Liaoning, China; Xi’an Institute of Mental Health, Xi’an, China; and Department of Mental Health, University of Aberdeen, Aberdeen, United Kingdom
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Chen Q, He G, Wang XY, Chen QY, Liu XM, Gu ZZ, Liu J, Li KQ, Wang SJ, Zhu SM, Feng GY, He L. Positive association between synapsin II and schizophrenia. Biol Psychiatry 2004; 56:177-81. [PMID: 15271586 DOI: 10.1016/j.biopsych.2004.05.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 04/23/2004] [Accepted: 05/19/2004] [Indexed: 01/11/2023]
Abstract
BACKGROUND Synapsin II encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. The expressions of messenger ribonucleic acid and protein of synapsin II have been reported to be significantly reduced in the brains of schizophrenia patients. The synapsin II gene is located on 3p25, a region that has been implicated to be associated with schizophrenia by genetic linkage. All these findings suggest synapsin II as a candidate gene for schizophrenia. METHODS In this work, we studied four markers (two single nucleotide polymorphisms (SNPs): rs308963 and rs795009; and two insertion/deletion polymorphisms: rs2307981 and rs2308169) covering 144.2 kilobase pairs (kb) with an average interval of 38 kb in synapsin II in a sample of 654 schizophrenic patients and 628 normal control subjects to explore the mechanism underlying schizophrenia. RESULTS We found significant differences in allele frequency distribution of SNP rs795009 (p =.000018, odds ratio 1.405, 95% confidence interval 1.202-1.641) between patients and control subjects. The T allele was significantly higher in patients than in control subjects. Moreover, the overall frequency of haplotype showed significant differences between patients and control subjects (p <.000001). CONCLUSIONS This study suggests a positive association between synapsin II and schizophrenia, implying that synapsin II is involved in the etiology of schizophrenia.
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Affiliation(s)
- Qi Chen
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, Shanghai, China
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35
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Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckmann JS. Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins 2004; 54:20-40. [PMID: 14705021 DOI: 10.1002/prot.10559] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Availability of complete genome sequences allows in-depth comparison of single-residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species-specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over- or underabundant across the whole proteomic landscape, as well as oligopeptides whose over- or underabundance is phylum- or species-specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection.
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Affiliation(s)
- Itsik Pe'er
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Abstract
We compared genes at which mutations are known to cause human disease (disease genes) with other human genes (nondisease genes) using a large set of human-rodent alignments to infer evolutionary patterns. Such comparisons may be of use both in predicting disease genes and in understanding the general evolution of human genes. Four features were found to differ significantly between disease and nondisease genes, with disease genes (i) evolving with higher nonsynonymous/synonymous substitution rate ratios (Ka/Ks), (ii) evolving at higher synonymous substitution rates, (iii) with longer protein-coding sequences, and (iv) expressed in a narrower range of tissues. Discriminant analysis showed that these differences may help to predict human disease genes. We also investigated other factors affecting the mode of evolution in the disease genes: Ka/Ks is significantly affected by protein function, mode of inheritance, and the reduction of life expectancy caused by disease.
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Affiliation(s)
- Nick G C Smith
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
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Cleaver JE, Collins C, Ellis J, Volik S. Genome sequence and splice site analysis of low-fidelity DNA polymerases H and I involved in replication of damaged DNA. Genomics 2003; 82:561-70. [PMID: 14559213 DOI: 10.1016/s0888-7543(03)00180-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
POLH and POLI are paralogs encoding low-fidelity, class Y, DNA polymerases involved in replication of damaged DNA in the human disease xeroderma pigmentosum variant. Analysis of genomic regions for human and mouse homologs, employing the analytic tool Genome Cryptographer, detected low-repetitive or unique regions at exons and other potential control regions, especially within intron I of human POLH. The human and mouse homologs are structurally similar, but the paralogs have undergone evolutionary divergence. The information content of splice sites for human POLH, the probability that a base would contribute to splicing, was low only for the acceptor site of exon II, which is preceded by a region of high information content that could contain sequences controlling splicing. This analysis explains previous observations of tissue-specific skipping during mRNA processing, resulting in the loss of the transcription start site in exon II, in human tissues.
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Affiliation(s)
- J E Cleaver
- UCSF Cancer Center, Box 0808, Room N431, University of California at San Francisco, San Francisco, CA 94143-0808, USA.
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