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Wang J, Wang Y, Jiang Y, Li S, Jia X, Xiao X, Sun W, Wang P, Zhang Q. Datasets-Based IMPDH1 Revisited: Heterozygous Missense Variants for Dominant Retinitis Pigmentosa While Truncation Variants Are Likely Non-Pathogenic. Curr Eye Res 2024:1-9. [PMID: 38604988 DOI: 10.1080/02713683.2024.2336158] [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: 04/19/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
PURPOSE Heterozygous variants of IMPDH1 are associated with autosomal dominant retinitis pigmentosa (adRP). The current study aims to investigate the characteristics of the adRP-associated variants. METHODS IMPDH1 variants from our exome sequencing dataset were retrieved and systemically evaluated through multiple online prediction tools, comparative genomics (in-house dataset, HGMD, and gnomAD), and phenotypic association. Potential pathogenic variants (PPVs) were further confirmed by Sanger sequencing and segregation analysis. RESULTS In total, seven heterozygous PPVs (six missenses and one inframe) were identified in 10 families with RP, in which six of the seven might be classified as pathogenic or likely pathogenic while one others as variants of uncertain significance. IMPDH1 variants contributed to 0.7% (10/1519) of RP families in our cohort, ranking the top four genes implicated in adRP. These adRP-associated variants were located in exons 8-10, a region within or downstream of the CBS domain. All these variants were predicted to be damaged by at least three of the six online prediction tools. Two truncation variants were considered non-pathogenic. Hitherto, 41 heterozygous variants of IMPDH1 were detected in 110 families in published literature, including 33 missenses, two inframes, and six truncations (including a synonymous variant affecting splicing). Of the 35 missense and inframe variants, most were clustered in exons 8-10 (77.1%, 27/35), including 18 (51.4%, 18/35) in exon 10 accounting for 70.9% (78/110) of the families. However, truncation variants were enriched in the general population with a pLI value of 0 (tolerated), and the reported variants in patients with RP did not cluster in specific region. CONCLUSIONS Our data together with comprehensive analysis of existing datasets suggest that causative variants of IMPDH1 are usually missense and mostly clustered in exons 8-10. Conversely, most missense variants outside this region and truncation variants should be interpreted with great care in clinical gene test.
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Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Department of Ophthalmology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guang-dong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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da Fonseca CAR, Prado VC, Paltian JJ, Kazmierczak JC, Schumacher RF, Sari MHM, Cordeiro LM, da Silva AF, Soares FAA, Oliboni RDS, Luchese C, Cruz L, Wilhelm EA. 4-(Phenylselanyl)-2H-chromen-2-one-Loaded Nanocapsule Suspension-A Promising Breakthrough in Pain Management: Comprehensive Molecular Docking, Formulation Design, and Toxicological and Pharmacological Assessments in Mice. Pharmaceutics 2024; 16:269. [PMID: 38399323 PMCID: PMC10892109 DOI: 10.3390/pharmaceutics16020269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Therapies for the treatment of pain and inflammation continue to pose a global challenge, emphasizing the significant impact of pain on patients' quality of life. Therefore, this study aimed to investigate the effects of 4-(Phenylselanyl)-2H-chromen-2-one (4-PSCO) on pain-associated proteins through computational molecular docking tests. A new pharmaceutical formulation based on polymeric nanocapsules was developed and characterized. The potential toxicity of 4-PSCO was assessed using Caenorhabditis elegans and Swiss mice, and its pharmacological actions through acute nociception and inflammation tests were also assessed. Our results demonstrated that 4-PSCO, in its free form, exhibited high affinity for the selected receptors, including p38 MAP kinase, peptidyl arginine deiminase type 4, phosphoinositide 3-kinase, Janus kinase 2, toll-like receptor 4, and nuclear factor-kappa β. Both free and nanoencapsulated 4-PSCO showed no toxicity in nematodes and mice. Parameters related to oxidative stress and plasma markers showed no significant change. Both treatments demonstrated antinociceptive and anti-edematogenic effects in the glutamate and hot plate tests. The nanoencapsulated form exhibited a more prolonged effect, reducing mechanical hypersensitivity in an inflammatory pain model. These findings underscore the promising potential of 4-PSCO as an alternative for the development of more effective and safer drugs for the treatment of pain and inflammation.
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Affiliation(s)
- Caren Aline Ramson da Fonseca
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Vinicius Costa Prado
- Graduate Program in Pharmaceutical Sciences, Pharmaceutical Technology Laboratory, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil;
| | - Jaini Janke Paltian
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Jean Carlo Kazmierczak
- Graduate Program in Chemistry, Chemistry Department, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (J.C.K.); (R.F.S.)
| | - Ricardo Frederico Schumacher
- Graduate Program in Chemistry, Chemistry Department, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (J.C.K.); (R.F.S.)
| | | | - Larissa Marafiga Cordeiro
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Aline Franzen da Silva
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Felix Alexandre Antunes Soares
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil; (L.M.C.); (A.F.d.S.); (F.A.A.S.)
| | - Robson da Silva Oliboni
- Center for Chemical, Pharmaceutical, and Food Sciences, CCQFA, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil;
| | - Cristiane Luchese
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
| | - Letícia Cruz
- Graduate Program in Pharmaceutical Sciences, Pharmaceutical Technology Laboratory, Federal University of Santa Maria, Santa Maria CEP 97105-900, RS, Brazil;
| | - Ethel Antunes Wilhelm
- Graduate Program in Biochemistry and Bioprospecting, Biochemical Pharmacology Research Laboratory, Federal University of Pelotas, Pelotas CEP 96010-900, RS, Brazil; (C.A.R.d.F.); (J.J.P.); (C.L.)
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Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [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: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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Xiang J, Peng J, Sun X, Lin Z, Li D, Ye H, Wang S, Bai Y, Wang X, Du P, Gao Y, Sun J, Pan S, Peng Z. The Next Generation of Population-Based DFNB16 Carrier Screening and Diagnosis: STRC Copy-Number Variant Analysis from Genome Sequencing Data. Clin Chem 2023:7174048. [PMID: 37207672 DOI: 10.1093/clinchem/hvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Deafness, autosomal recessive 16 (DFNB16) is caused by compound heterozygous or homozygous variants in STRC and is the second most common form of genetic hearing loss. Due to the nearly identical sequences of STRC and the pseudogene STRCP1, analysis of this region is challenging in clinical testing. METHODS We developed a method that accurately identifies the copy number of STRC and STRCP1 using standard short-read genome sequencing. Then, we used whole genome sequencing (WGS) data to investigate the population distribution of STRC copy number in 6813 neonates and the correlation between STRC and STRCP1 copy number. RESULTS The comparison of WGS results with multiplex ligation-dependent probe amplification demonstrated high sensitivity (100%; 95% CI, 97.5%-100%) and specificity (98.8%; 95% CI, 97.7%-99.5%) in detecting heterozygous deletion of STRC from short-read genome sequencing data. The population analysis revealed that 5.22% of the general population has STRC copy number changes, almost half of which (2.33%; 95% CI, 1.99%-2.72%) were clinically significant, including heterozygous and homozygous STRC deletions. There was a strong inverse correlation between STRC and STRCP1 copy number. CONCLUSIONS We developed a novel and reliable method to determine STRC copy number based on standard short-read based WGS data. Incorporating this method into analytic pipelines would improve the clinical utility of WGS in the screening and diagnosis of hearing loss. Finally, we provide population-based evidence of pseudogene-mediated gene conversions between STRC and STRCP1.
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Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Zibin Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haodong Ye
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Sibao Wang
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266034, China
| | - Yushi Bai
- Guangdong Zhongyi Forensic Science Center, Shenzhen 518000, China
| | | | - Peina Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Silin Pan
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266034, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Abrahamsson S, Eiengård F, Rohlin A, Dávila López M. PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data. BMC Bioinformatics 2022; 23:59. [PMID: 35114952 PMCID: PMC8812246 DOI: 10.1186/s12859-022-04583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders. RESULTS We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene. CONCLUSIONS PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.
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Affiliation(s)
- Sanna Abrahamsson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 115, 405 30, Gothenburg, Sweden
| | - Frida Eiengård
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Rohlin
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Unit of Genetic Analysis and Bioinformatics, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marcela Dávila López
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 115, 405 30, Gothenburg, Sweden.
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Pseudogenes: Four Decades of Discovery. Methods Mol Biol 2021. [PMID: 34165705 DOI: 10.1007/978-1-0716-1503-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
A pseudogene is defined as a genomic DNA sequence that looks like a mutated or truncated version of a known functional gene. Nearly four decades since their first discovery it has been estimated that between ~12,000 and ~20,000 pseudogenes exist in the human genome. Early efforts to characterize functions for pseudogenes were unsuccessful, thus they were considered functionless relics of evolutionary selection, junk DNA or genetic fossils. Remarkably, an increasing number of pseudogenes have been reported to be expressed as RNA transcripts above and beyond levels considered accidental or spurious transcription. There is emerging evidence that some expressed pseudogene transcripts have biological functions and should be defined as a subclass of functional long noncoding RNAs (lncRNA). In this introductory chapter, I briefly summarize the history and the current knowledge of pseudogenes, and highlight the emerging functions of some pseudogenes in human biology and disease. This second iteration of Pseudogenes in Methods in Molecular Biology highlights new methodological approaches to investigate this intriguing family of lncRNAs and the extent of their biological function.
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Stephens Z, Milosevic D, Kipp B, Grebe S, Iyer RK, Kocher JPA. PB-Motif-A Method for Identifying Gene/Pseudogene Rearrangements With Long Reads: An Application to CYP21A2 Genotyping. Front Genet 2021; 12:716586. [PMID: 34394200 PMCID: PMC8355628 DOI: 10.3389/fgene.2021.716586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022] Open
Abstract
Long read sequencing technologies have the potential to accurately detect and phase variation in genomic regions that are difficult to fully characterize with conventional short read methods. These difficult to sequence regions include several clinically relevant genes with highly homologous pseudogenes, many of which are prone to gene conversions or other types of complex structural rearrangements. We present PB-Motif, a new method for identifying rearrangements between two highly homologous genomic regions using PacBio long reads. PB-Motif leverages clustering and filtering techniques to efficiently report rearrangements in the presence of sequencing errors and other systematic artifacts. Supporting reads for each high-confidence rearrangement can then be used for copy number estimation and phased variant calling. First, we demonstrate PB-Motif's accuracy with simulated sequence rearrangements of PMS2 and its pseudogene PMS2CL using simulated reads sweeping over a range of sequencing error rates. We then apply PB-Motif to 26 clinical samples, characterizing CYP21A2 and its pseudogene CYP21A1P as part of a diagnostic assay for congenital adrenal hyperplasia. We successfully identify damaging variation and patient carrier status concordant with clinical diagnosis obtained from multiplex ligation-dependent amplification (MLPA) and Sanger sequencing. The source code is available at: github.com/zstephens/pb-motif.
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Affiliation(s)
- Zachary Stephens
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | | | | | | | - Ravishankar K Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
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Zhang X, Song X, Lai Y, Zhu B, Luo J, Yu H, Yu Y. Identification of key pseudogenes in nasopharyngeal carcinoma based on RNA-Seq analysis. BMC Cancer 2021; 21:483. [PMID: 33931030 PMCID: PMC8088053 DOI: 10.1186/s12885-021-08211-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/13/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a malignant head and neck tumor, and more than 70% of new cases are in East and Southeast Asia. However, association between NPC and pseudogenes playing important roles in genesis of multiple tumor types is still not clear and needs to be investigated. METHODS Using RNA-Sequencing (RNA-seq) technology, we analyzed pseudogene expression in 13 primary NPC and 6 recurrent NPC samples as well as their paracancerous counterparts. Quantitative PCR was used to validate the differentially expressed pseudogenes. RESULTS We found 251 differentially expressed pseudogenes including 73 up-regulated and 178 down-regulated ones between primary NPC and paracancerous tissues. Enrichment analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted to filter out the key pseudogenes. We reported that pseudogenes from cytochrome P450 (CYP) family, such as CYP2F2P, CYP2G1P, CYP4F24P, CYP2B7P and CYP2G2P were significantly down-regulated in NPC compared to paracancerous tissues, while IGHV1OR15-2, IGHV3-11, FCGR1CP and IGHV3-69-1 belonging to Fc gamma receptors were significantly up-regulated. CYP2B7P, CYP2F2P and CYP4F26P were enriched in arachidonic acid metabolism pathway. The qRT-PCR analysis validated the lower expression of pseudogenes CYP2F2P and CYP2B7P in NPC tissues and cell lines compared to paracancerous tissues and normal human nasopharyngeal epithelial cell line. CYP2B7P overexpression weakened migratory and invasive capacity of NPC cell line. Moreover, the expression pattern of those pseudogenes in recurrent NPC tissues was different from the primary NPC. CONCLUSION This study suggested the role of pseudogenes in tumorigenesis and progression, potentially functioning as therapeutic targets to NPC.
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Affiliation(s)
- Xiujuan Zhang
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China
| | - Xiaole Song
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China
| | - Yuting Lai
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China
| | - Bijun Zhu
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China
| | - Jiqin Luo
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China
| | - Hongmeng Yu
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China. .,Research Units of New Technologies of Endoscopic Surgery in Skull Base Tumor, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Yiqun Yu
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, 83 Fen Yang Road, Shanghai, 200031, China.
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Shukla S, Srividya K, Nazir A. Not a piece of junk anymore: Pseudogene T04B2.1 performs non-conventional regulatory role and modulates aggregation of α- synuclein and β-amyloid proteins in C. elegans. Biochem Biophys Res Commun 2021; 539:8-14. [PMID: 33412418 DOI: 10.1016/j.bbrc.2020.12.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022]
Abstract
The conventional notions of pseudogenes being 'junk DNA' have largely been offset as research studies have established their role in multiple biological processes. Our studies towards identification of genetic modulators employing C. elegans model, that associate reproductive health and age-related neurodegenerative diseases, led us to identification and functional characterization of a pseudogene T04B2.1, which when knocked down, exacerbates the aggregation of α-Synuclein and β-Amyloid proteins, induces lipid deposition and alters morphometric endpoints in worms. Whole transcriptome analysis of worms under knockdown condition of T04B2.1 revealed an altered expression of 187 sequences, most of these being non-coding RNAs, miRNAs and piRNAs modulating the RNAi regulatory processes. Our gene ontology and pathway enrichment analysis demonstrated the role of T04B2.1 in protein quality control, metabolic pathways and development. We further performed a signature motif search and successfully identified a common motif that is present between all piRNA and miRNA molecules, which are significantly altered upon T04B2.1 silencing. This study unveils the non-conventional regulatory role of pseudogene T04B2.1 with respect to effects associated with neurodegenerative diseases and encourages further studies to decipher the regulatory mechanism governed by pseudogenes.
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Affiliation(s)
- Shikha Shukla
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Kottapalli Srividya
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
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Bok I, Karreth FA. Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer. Methods Mol Biol 2021; 2324:287-304. [PMID: 34165722 DOI: 10.1007/978-1-0716-1503-4_18] [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] [Indexed: 06/13/2023]
Abstract
Aberrant expression of pseudogenes has been observed in many cancer types. Deregulated pseudogenes engage in a multitude of biological processes at the DNA, RNA, and protein levels and eventually facilitate disease progression. To investigate pseudogene functions in cancer, cell lines and cell line transplantation models have been widely used. However, cancer biology is best studied in the context of an intact organism. Here, we present various strategies to investigate pseudogenes in genetically engineered mouse models and discuss advantages and disadvantages of the different approaches.
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Affiliation(s)
- Ilah Bok
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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11
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Dainat J, Pontarotti P. Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach. Methods Mol Biol 2021; 2324:21-34. [PMID: 34165706 DOI: 10.1007/978-1-0716-1503-4_2] [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] [Indexed: 06/13/2023]
Abstract
The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.
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Affiliation(s)
- Jacques Dainat
- Department of Medical Biochemistry Microbiology and Genomics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Pierre Pontarotti
- Aix Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, Marseille, France
- SNC5039 CNRS, Marseille, France
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12
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Abstract
Pseudogenes are commonly labeled as "junk DNA" given their perceived nonfunctional status. However, the advent of large-scale genomics projects prompted a revisit of pseudogene biology, highlighting their key functional and regulatory roles in numerous diseases, including cancers. Integrative analyses of cancer data have shown that pseudogenes can be transcribed and even translated, and that pseudogenic DNA, RNA, and proteins can interfere with the activity and function of key protein coding genes, acting as regulators of oncogenes and tumor suppressors. Capitalizing on the available clinical research, we are able to get an insight into the spread and variety of pseudogene biomarker and therapeutic potential. In this chapter, we describe pseudogenes that fulfill their role as diagnostic or prognostic biomarkers, both as unique elements and in collaboration with other genes or pseudogenes. We also report that the majority of prognostic pseudogenes are overexpressed and exert an oncogenic role in colorectal, liver, lung, and gastric cancers. Finally, we highlight a number of pseudogenes that can establish future therapeutic avenues.
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13
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Wrona D, Pastukhov O, Pritchard RS, Raimondi F, Tchinda J, Jinek M, Siler U, Reichenbach J. CRISPR-Directed Therapeutic Correction at the NCF1 Locus Is Challenged by Frequent Incidence of Chromosomal Deletions. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:936-943. [PMID: 32420407 PMCID: PMC7217921 DOI: 10.1016/j.omtm.2020.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
Resurrection of non-processed pseudogenes may increase the efficacy of therapeutic gene editing, upon simultaneous targeting of a mutated gene and its highly homologous pseudogenes. To investigate the potency of this approach for clinical gene therapy of human diseases, we corrected a pseudogene-associated disorder, the immunodeficiency p47phox-deficient chronic granulomatous disease (p47phox CGD), using clustered regularly interspaced short palindromic repeats-associated nuclease Cas9 (CRISPR-Cas9) to target mutated neutrophil cytosolic factor 1 (NCF1). Being separated by less than two million base pairs, NCF1 and two pseudogenes are closely co-localized on chromosome 7. In healthy people, a two-nucleotide GT deletion (ΔGT) is present in the NCF1B and NCF1C pseudogenes only. In the majority of patients with p47phox CGD, the NCF1 gene is inactivated due to a ΔGT transfer from one of the two non-processed pseudogenes. Here we demonstrate that concurrent targeting and correction of mutated NCF1 and its pseudogenes results in therapeutic CGD phenotype correction, but also causes potentially harmful chromosomal deletions between the targeted loci in a p47phox-deficient CGD cell line model. Therefore, development of genome-editing-based treatment of pseudogene-related disorders mandates thorough safety examination, as well as technological advances, limiting concurrent induction of multiple double-strand breaks on a single chromosome.
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Affiliation(s)
- Dominik Wrona
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Oleksandr Pastukhov
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | | | - Federica Raimondi
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Joëlle Tchinda
- Department of Oncology, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Ulrich Siler
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Janine Reichenbach
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland
- Department of Somatic Gene Therapy, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Children’s Research Center, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Corresponding author: Janine Reichenbach, Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, 8952 Schlieren-Zurich, Switzerland.
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14
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Molecular fossils “pseudogenes” as functional signature in biological system. Genes Genomics 2020; 42:619-630. [DOI: 10.1007/s13258-020-00935-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
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15
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Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet 2019; 21:191-201. [DOI: 10.1038/s41576-019-0196-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 01/08/2023]
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16
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Maranda V, Sunstrum FG, Drouin G. Both male and female gamete generating cells produce processed pseudogenes in the human genome. Gene 2018; 684:70-75. [PMID: 30359744 DOI: 10.1016/j.gene.2018.10.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 11/25/2022]
Abstract
The human genome contains an unusually large number of processed pseudogenes. The fact that processed pseudogenes are roughly 33% more abundant in our X chromosome than in our autosomes suggests that this overabundance is the result of the fact that human oogenesis is much longer than that of non-mammalian species. Here, we analyze the origins of the processed pseudogenes found on the human Y chromosome to determine whether human spermatogenesis also contribute to this overabundance. Our results show that human processed pseudogenes not only retrotranspose to the Y chromosome, but are also produced by genes on the Y chromosome. Furthermore, the fact that X chromosomes are three times more abundant than Y chromosomes likely explains why the euchromatic density of processed pseudogenes is three times higher in the X chromosome than in the Y chromosome. The large number of processed pseudogenes found in our genome is therefore due to the low substrate specificity of the L1 reverse transcriptase responsible for the reverse transcription of germline mRNA molecules into processed pseudogenes, as well as the life-long production of both male and female gametes.
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Affiliation(s)
- Vincent Maranda
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Frédérick G Sunstrum
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Guy Drouin
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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17
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Tsairidou S, Allen AR, Pong‐Wong R, McBride SH, Wright DM, Matika O, Pooley CM, McDowell SWJ, Glass EJ, Skuce RA, Bishop SC, Woolliams JA. An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance. Anim Genet 2018; 49:103-109. [PMID: 29368428 PMCID: PMC5888165 DOI: 10.1111/age.12637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 12/13/2022]
Abstract
Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non-additive genetic variation, we present an approach using genome-wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein-Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome-wide markers were tested for associations between heterozygosity and bTB status using marker-based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy-Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome-wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy-number-variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large-scale data.
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Affiliation(s)
- S. Tsairidou
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - A. R. Allen
- Veterinary Sciences DivisionAgri‐Food and Biosciences InstituteBelfastBT95PXUK
| | - R. Pong‐Wong
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - S. H. McBride
- Veterinary Sciences DivisionAgri‐Food and Biosciences InstituteBelfastBT95PXUK
| | - D. M. Wright
- School of Biological SciencesQueen's University of BelfastBelfastBT71NNUK
| | - O. Matika
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - C. M. Pooley
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - S. W. J. McDowell
- Veterinary Sciences DivisionAgri‐Food and Biosciences InstituteBelfastBT95PXUK
| | - E. J. Glass
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - R. A. Skuce
- Veterinary Sciences DivisionAgri‐Food and Biosciences InstituteBelfastBT95PXUK
- School of Biological SciencesQueen's University of BelfastBelfastBT71NNUK
| | - S. C. Bishop
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
| | - J. A. Woolliams
- The Roslin Institute and R(D)SVSUniversity of EdinburghEdinburghEH259RGUK
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18
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Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet 2017; 93:439-449. [PMID: 28950406 DOI: 10.1111/cge.13146] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Genomic disorders result from copy-number variants (CNVs) or submicroscopic rearrangements of the genome rather than from single nucleotide variants (SNVs). Diverse technologies, including array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) microarrays, and more recently, whole genome sequencing and whole-exome sequencing, have enabled robust genome-wide unbiased detection of CNVs in affected individuals and in reportedly healthy controls. Sequencing of breakpoint junctions has allowed for elucidation of upstream mechanisms leading to genomic instability and resultant structural variation, whereas studies of the association between CNVs and specific diseases or susceptibility to morbid traits have enhanced our understanding of the downstream effects. In this review, we discuss the hallmarks of genomic disorders as they were defined during the first decade of the field, including genomic instability and the mechanism for rearrangement defined as nonallelic homologous recombination (NAHR); recurrent vs nonrecurrent rearrangements; and gene dosage sensitivity. Moreover, we highlight the exciting advances of the second decade of this field, including a deeper understanding of genomic instability and the mechanisms underlying complex rearrangements, mechanisms for constitutional and somatic chromosomal rearrangements, structural intra-species polymorphisms and susceptibility to NAHR, the role of CNVs in the context of genome-wide copy number and single nucleotide variation, and the contribution of noncoding CNVs to human disease.
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Affiliation(s)
- T Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - J R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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19
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Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates. Proc Natl Acad Sci U S A 2017; 114:12779-12784. [PMID: 29138319 DOI: 10.1073/pnas.1708151114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Gene conversion is the copying of a genetic sequence from a "donor" region to an "acceptor." In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of [Formula: see text] per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge-until an eventual "escape" of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.
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20
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snRNP proteins in health and disease. Semin Cell Dev Biol 2017; 79:92-102. [PMID: 29037818 DOI: 10.1016/j.semcdb.2017.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
Abstract
Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.
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21
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Gemayel KT, Litman GW, Sriaroon P. Autosomal recessive agammaglobulinemia associated with an IGLL1 gene missense mutation. Ann Allergy Asthma Immunol 2016; 117:439-441. [PMID: 27576013 DOI: 10.1016/j.anai.2016.07.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/25/2016] [Accepted: 07/30/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Kristina T Gemayel
- Nova Southeastern University, College of Osteopathic Medicine, Fort Lauderdale, Florida
| | - Gary W Litman
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, University of South Florida Morsani College of Medicine, Saint Petersburg, Florida
| | - Panida Sriaroon
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, University of South Florida Morsani College of Medicine, Saint Petersburg, Florida.
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22
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Abstract
A majority of human genes contain non-coding intervening sequences – introns that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases are caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations.
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Affiliation(s)
- Šárka Růžičková
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
| | - David Staněk
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
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23
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Kavakiotis I, Xochelli A, Agathangelidis A, Tsoumakas G, Maglaveras N, Stamatopoulos K, Hadzidimitriou A, Vlahavas I, Chouvarda I. Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia. BMC Bioinformatics 2016; 17 Suppl 5:173. [PMID: 27295298 PMCID: PMC4905615 DOI: 10.1186/s12859-016-1044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insight into the physiology and pathology of B cells, leading to strong prognostication markers for clinical outcome in chronic lymphocytic leukaemia (CLL), the most frequent adult B-cell malignancy. In this paper we present a methodology for integrating multiple immunogenetic and clinocobiological data sources in order to extract features and create high quality datasets for SHM analysis in IG receptors of CLL patients. This dataset is used as the basis for a higher level integration procedure, inspired form social choice theory. This is applied in the Towards Analysis, our attempt to investigate the potential ontogenetic transformation of genes belonging to specific stereotyped CLL subsets towards other genes or gene families, through SHM. RESULTS The data integration process, followed by feature extraction, resulted in the generation of a dataset containing information about mutations occurring through SHM. The Towards analysis performed on the integrated dataset applying voting techniques, revealed the distinct behaviour of subset #201 compared to other subsets, as regards SHM related movements among gene clans, both in allele-conserved and non-conserved gene areas. With respect to movement between genes, a high percentage movement towards pseudo genes was found in all CLL subsets. CONCLUSIONS This data integration and feature extraction process can set the basis for exploratory analysis or a fully automated computational data mining approach on many as yet unanswered, clinically relevant biological questions.
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Affiliation(s)
- Ioannis Kavakiotis
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Agathangelidis
- Division of Molecular Oncology and Department of Onco-Hematology, San Raffaele Scientific Institute, Milan, Italy
| | - Grigorios Tsoumakas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nicos Maglaveras
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ioannis Vlahavas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioanna Chouvarda
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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24
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Mandelker D, Schmidt RJ, Ankala A, McDonald Gibson K, Bowser M, Sharma H, Duffy E, Hegde M, Santani A, Lebo M, Funke B. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing. Genet Med 2016; 18:1282-1289. [PMID: 27228465 DOI: 10.1038/gim.2016.58] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 03/24/2016] [Indexed: 01/25/2023] Open
Abstract
PURPOSE Next-generation sequencing (NGS) is now routinely used to interrogate large sets of genes in a diagnostic setting. Regions of high sequence homology continue to be a major challenge for short-read technologies and can lead to false-positive and false-negative diagnostic errors. At the scale of whole-exome sequencing (WES), laboratories may be limited in their knowledge of genes and regions that pose technical hurdles due to high homology. We have created an exome-wide resource that catalogs highly homologous regions that is tailored toward diagnostic applications. METHODS This resource was developed using a mappability-based approach tailored to current Sanger and NGS protocols. RESULTS Gene-level and exon-level lists delineate regions that are difficult or impossible to analyze via standard NGS. These regions are ranked by degree of affectedness, annotated for medical relevance, and classified by the type of homology (within-gene, different functional gene, known pseudogene, uncharacterized noncoding region). Additionally, we provide a list of exons that cannot be analyzed by short-amplicon Sanger sequencing. CONCLUSION This resource can help guide clinical test design, supplemental assay implementation, and results interpretation in the context of high homology.Genet Med 18 12, 1282-1289.
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Affiliation(s)
- Diana Mandelker
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA.,Current affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA (D.M.); Medical Genetics, Invitae Corporation, San Francisco, California, USA (K.M.G.)
| | - Ryan J Schmidt
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kristin McDonald Gibson
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Current affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA (D.M.); Medical Genetics, Invitae Corporation, San Francisco, California, USA (K.M.G.)
| | - Mark Bowser
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Himanshu Sharma
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Elizabeth Duffy
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Madhuri Hegde
- Emory Genetics Lab, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew Lebo
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts, USA.,Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Birgit Funke
- Partners HealthCare Personalized Medicine, Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School/Massachusetts General Hospital, Boston, Massachusetts, USA
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25
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Dumont BL. Interlocus gene conversion explains at least 2.7% of single nucleotide variants in human segmental duplications. BMC Genomics 2015; 16:456. [PMID: 26077037 PMCID: PMC4467073 DOI: 10.1186/s12864-015-1681-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/01/2015] [Indexed: 01/24/2023] Open
Abstract
Background Interlocus gene conversion (IGC) is a recombination-based mechanism that results in the unidirectional transfer of short stretches of sequence between paralogous loci. Although IGC is a well-established mechanism of human disease, the extent to which this mutagenic process has shaped overall patterns of segregating variation in multi-copy regions of the human genome remains unknown. One expected manifestation of IGC in population genomic data is the presence of one-to-one paralogous SNPs that segregate identical alleles. Results Here, I use SNP genotype calls from the low-coverage phase 3 release of the 1000 Genomes Project to identify 15,790 parallel, shared SNPs in duplicated regions of the human genome. My approach for identifying these sites accounts for the potential redundancy of short read mapping in multi-copy genomic regions, thereby effectively eliminating false positive SNP calls arising from paralogous sequence variation. I demonstrate that independent mutation events to identical nucleotides at paralogous sites are not a significant source of shared polymorphisms in the human genome, consistent with the interpretation that these sites are the outcome of historical IGC events. These putative signals of IGC are enriched in genomic contexts previously associated with non-allelic homologous recombination, including clear signals in gene families that form tandem intra-chromosomal clusters. Conclusions Taken together, my analyses implicate IGC, not point mutation, as the mechanism generating at least 2.7 % of single nucleotide variants in duplicated regions of the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1681-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Beth L Dumont
- Initiative in Biological Complexity, North Carolina State University, 112 Derieux Place, 3510 Thomas Hall, Campus Box 7614, Raleigh, NC, 27695-7614, USA.
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26
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Abstract
Pseudogenes were once considered genomic fossils, but recent studies indicate that they may function as gene regulators through the generation of endogenous small interfering RNAs (esiRNAs), antisense RNAs, and decoys for microRNAs. In this review, we summarize pseudogene study methods, emphasizing relevant publicly available resources, and we describe a systematic pipeline to identify pseudogene-derived esiRNAs and their targets, which can lead to a deeper understanding of pseudogene function.
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Affiliation(s)
- Wen-Ling Chan
- Biomedical Informatics, Asia University, Taichung, Taiwan
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27
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Sampathkumar G, Drouin G. Purifying selection against gene conversions between the polyamine transport (TPO) genes of Saccharomyces species. Curr Genet 2014; 61:67-72. [DOI: 10.1007/s00294-014-0445-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/06/2014] [Accepted: 08/09/2014] [Indexed: 10/24/2022]
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28
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Vitiello M, Tuccoli A, Poliseno L. Long non-coding RNAs in cancer: implications for personalized therapy. Cell Oncol (Dordr) 2014; 38:17-28. [PMID: 25113790 DOI: 10.1007/s13402-014-0180-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2014] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs, pseudogenes and circRNAs) have recently come into light as powerful players in cancer pathogenesis and it is becoming increasingly clear that they have the potential of greatly contributing to the spread and success of personalized cancer medicine. In this concise review, we briefly introduce these three classes of long non-coding RNAs. We then discuss their applications as diagnostic and prognostic biomarkers. Finally, we describe their appeal as targets and as drugs, while pointing out the limitations that still lie ahead of their definitive entry into clinical practice.
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Affiliation(s)
- Marianna Vitiello
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori c/o IFC-CNR, via Moruzzi 1, 56124, Pisa, Italy
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29
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Piscopo SP, Drouin G. [High gene conversion frequency between genes encoding 2-deoxyglucose-6-phosphate phosphatase in 3 Saccharomyces species]. Genome 2014; 57:303-8. [PMID: 25188289 DOI: 10.1139/gen-2014-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gene conversions are nonreciprocal sequence exchanges between genes. They are relatively common in Saccharomyces cerevisiae, but few studies have investigated the evolutionary fate of gene conversions or their functional impacts. Here, we analyze the evolution and impact of gene conversions between the two genes encoding 2-deoxyglucose-6-phosphate phosphatase in S. cerevisiae, Saccharomyces paradoxus and Saccharomyces mikatae. Our results demonstrate that the last half of these genes are subject to gene conversions among these three species. The greater similarity and the greater percentage of GC nucleotides in the converted regions, as well as the absence of long regions of adjacent common converted sites, suggest that these gene conversions are frequent and occur independently in all three species. The high frequency of these conversions probably result from the fact that they have little impact on the protein sequences encoded by these genes.
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Affiliation(s)
- Sara-Pier Piscopo
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
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30
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Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Hum Genet 2014; 133:1255-71. [DOI: 10.1007/s00439-014-1460-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/03/2014] [Indexed: 12/01/2022]
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31
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Dainat J, Pontarotti P. Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach. Methods Mol Biol 2014; 1167:87-99. [PMID: 24823773 DOI: 10.1007/978-1-4939-0835-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
During the last few years, the study of pseudogenes has excited enthusiasm, because it has been proven that at least some of them are involved in important biological processes. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow studying pseudogene history are described.
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Affiliation(s)
- Jacques Dainat
- Evolutionary Biology and Modeling Group, Aix-Marseille Université, LATP - UMR 7353, 3 Place Victor Hugo - Case 19, 13331, Marseille Cedex 3, France,
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32
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Abstract
The number of complete genome sequences explodes more and more with each passing year. Thus, methods for genome annotation need to be honed constantly to handle the deluge of information. Annotation of pseudogenes (i.e., gene copies that appear not to make a functional protein) in genomes is a persistent problem; here, we overview pseudogene annotation methods that are based on the detection of sequence homology in genomic DNA.
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Affiliation(s)
- Paul M Harrison
- Department of Biology, McGill University, Stewart Biology Building, 1205 Doctor Penfield Avenue, Montreal, QC, Canada, H3A 1B1,
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33
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Abstract
The study of pseudogenes, originally dismissed as genomic relics of evolutionary selection, has seen a resurgence in scientific literature, in addition to being a peculiar topic of discussion in theological debates. For a long time, pseudogenes have been touted as a beacon of natural selection and a definitive proof of evolution due to the slow mutation rate that differentiated them from their parental genes and ultimately caused their genetic demise as functional genes. It now seems that "creationists" have co-opted some recent reports identifying unheralded biological functions to pseudogens and other noncoding RNAs as evidence to undermine the existence of evolution and supporting intelligent design. This issue of Methods in Molecular Biology focused on pseudogenes will certainly not end, nor enter this debate; however, scientists who are also genomics and pseudogene enthusiasts will certainly appreciate that many scientists are thinking about these particular genetic elements in new and interesting ways. With this new interest in a biological significance and "non-junk" role for pseudogenes and other noncoding RNAs, new methods and approaches are being developed to unlock the mystery of these ancient artifacts we know as pseudogenes. In this brief introductory chapter we highlight the renewed interest in pseudogenes and review a rationale for intensification of pseudogene-related research.
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Balakirev ES, Chechetkin VR, Lobzin VV, Ayala FJ. Computational methods of identification of pseudogenes based on functionality: entropy and GC content. Methods Mol Biol 2014; 1167:41-62. [PMID: 24823770 DOI: 10.1007/978-1-4939-0835-6_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene-pseudogene evolution.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA,
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35
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Lee HH. Mutational analysis of CYP21A2 gene and CYP21A1P pseudogene: long-range PCR on genomic DNA. Methods Mol Biol 2014; 1167:275-87. [PMID: 24823785 DOI: 10.1007/978-1-4939-0835-6_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
CYP21A2, the gene that codes for P450c21 (Steroid 21-hydroxylase), has a duplicated pseudogene called CYP21A1P. The gene and the pseudogene share 98 % and 96 % sequence homology in exons and in noncoding sequences, respectively, and are located 30 kb apart within the HLA class III human histocompatibility complex locus on chromosome 6p21.3. CYP21A1P is inactive due to the presence of 11 deteriorated mutations in its coding region. These mutations can be transferred to the functional CYP21A2 through intergenic recombination during meiosis or mitosis and lead to the congenital adrenal hyperplasia (CAH) resulting from 21-hydroxylase deficiency. Conversely, portions of CYP21A2 sequence can be transferred to CYP21A1P, modifying the haplotype. Here, we describe a well-established protocol that can be used to unambiguously study the mutational profile of CYP21A2 gene and CYP21A1P pseudogene. The protocol is based on long-range PCR amplification with allele-specific primers, followed by DNA sequencing of smaller fragments.
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Affiliation(s)
- Hsien-Hsiung Lee
- Department of Laboratory Medicine, China Medical University Hospital, 2 Yuh-Der Road, Taichung, 404, Taiwan,
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36
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Petronella N, Drouin G. Purifying selection against gene conversions in the folate receptor genes of primates. Genomics 2013; 103:40-7. [PMID: 24184359 DOI: 10.1016/j.ygeno.2013.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/20/2013] [Accepted: 10/22/2013] [Indexed: 01/07/2023]
Abstract
We characterized the gene conversions between the human folate receptor (FOLR) genes and those of five other primate species. We found 26 gene conversions having an average length of 534 nucleotides. The length of these conversions is correlated with sequence similarity, converted regions have a higher GC-content and the average size of converted regions from a functional donor to another functional donor is significantly smaller than the average size from a functional donor to a pseudogene. Furthermore, the few conversions observed in the FOLR1 and FOLR2 genes did not change any amino acids in their coding regions and did not affect their promoter regions. In contrast, the promoter and coding regions of the FOLR3 gene are frequently converted and these conversions changed many amino acids in marmoset. These results suggest that purifying selection is limiting the functional impact that frequent gene conversions have on functional folate receptor genes.
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Affiliation(s)
- Nicholas Petronella
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Guy Drouin
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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37
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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Chan WL, Yang WK, Huang HD, Chang JG. pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat001. [PMID: 23396300 PMCID: PMC3567485 DOI: 10.1093/database/bat001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/. Database URL:http://pseudomap.mbc.nctu.edu.tw/
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Affiliation(s)
- Wen-Ling Chan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan
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39
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Abstract
Because they are generally noncoding and thus considered nonfunctional and unimportant, pseudogenes have long been neglected. Recent advances have established that the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. Therefore, pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression, with a multifaceted involvement in the pathogenesis of human cancer.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori (CRL-ITT), c/o IFC-CNR Via Moruzzi 1, 56124 Pisa, Italy.
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40
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Marotta M, Piontkivska H, Tanaka H. Molecular trajectories leading to the alternative fates of duplicate genes. PLoS One 2012; 7:e38958. [PMID: 22720000 PMCID: PMC3375281 DOI: 10.1371/journal.pone.0038958] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/14/2012] [Indexed: 11/21/2022] Open
Abstract
Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.
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Affiliation(s)
- Michael Marotta
- Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, Ohio, United States of America
| | - Hisashi Tanaka
- Department of Molecular Genetics, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
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41
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Abstract
Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene transcripts may also form small interfering RNA or decrease cellular miRNA concentration. Thus, pseudogenes regulate tumor suppressors and oncogenes. Their essential functions draw the attention of our research group in my current work on heat shock protein 90: a chaperone of oncogenes. The paper reviews our current knowledge on pseudogenes and evaluates preliminary results of the chaperone data. Current efforts to understand pseudogenes interactions help to understand the functions of a genome.
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42
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Sen K, Ghosh TC. Evolutionary conservation and disease gene association of the human genes composing pseudogenes. Gene 2012; 501:164-70. [PMID: 22521745 DOI: 10.1016/j.gene.2012.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/09/2012] [Accepted: 04/05/2012] [Indexed: 01/16/2023]
Abstract
Pseudogenes, the 'genomic fossils' present portrayal of evolutionary history of human genome. The human genes configuring pseudogenes are also now coming forth as important resources in the study of human protein evolution. In this communication, we explored evolutionary conservation of the genes forming pseudogenes over the genes lacking any pseudogene and delving deeper, we probed an evolutionary rate difference between the disease genes in the two groups. We illustrated this differential evolutionary pattern by gene expressivity, number of regulatory miRNA targeting per gene, abundance of protein complex forming genes and lesser percentage of protein intrinsic disorderness. Furthermore, pseudogenes are observed to harbor sequence variations, over their entirety, those become degenerative disease-causing mutations though the disease involvement of their progenitors is still unexplored. Here, we unveiled an immense association of disease genes in the genes casting pseudogenes in human. We interpreted the issue by disease associated miRNA targeting, genes containing polymorphisms in miRNA target sites, abundance of genes having disease causing non-synonymous mutations, disease gene specific network properties, presence of genes having repeat regions, affluence of dosage sensitive genes and the presence of intrinsically unstructured protein regions.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
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43
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Rossetti S, Hopp K, Sikkink RA, Sundsbak JL, Lee YK, Kubly V, Eckloff BW, Ward CJ, Winearls CG, Torres VE, Harris PC. Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing. J Am Soc Nephrol 2012; 23:915-33. [PMID: 22383692 DOI: 10.1681/asn.2011101032] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Mutations in two large multi-exon genes, PKD1 and PKD2, cause autosomal dominant polycystic kidney disease (ADPKD). The duplication of PKD1 exons 1-32 as six pseudogenes on chromosome 16, the high level of allelic heterogeneity, and the cost of Sanger sequencing complicate mutation analysis, which can aid diagnostics of ADPKD. We developed and validated a strategy to analyze both the PKD1 and PKD2 genes using next-generation sequencing by pooling long-range PCR amplicons and multiplexing bar-coded libraries. We used this approach to characterize a cohort of 230 patients with ADPKD. This process detected definitely and likely pathogenic variants in 115 (63%) of 183 patients with typical ADPKD. In addition, we identified atypical mutations, a gene conversion, and one missed mutation resulting from allele dropout, and we characterized the pattern of deep intronic variation for both genes. In summary, this strategy involving next-generation sequencing is a model for future genetic characterization of large ADPKD populations.
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Affiliation(s)
- Sandro Rossetti
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA.
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Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW. Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease. Genome Res 2012; 22:429-35. [PMID: 22090377 PMCID: PMC3290778 DOI: 10.1101/gr.127738.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 11/15/2011] [Indexed: 01/06/2023]
Abstract
Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature, and clinical sequelae of genetic disorders in humans. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. However, pathological mutations can also be introduced by nonreciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have thus far been linked to pathology in more than 20 human genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. Here, we have used a genome-wide computational approach to identify disease-associated mutations derived from IGC events. Our approach revealed hundreds of known pathological mutations that could have been caused by IGC. Further, we identified several dozen high-confidence cases of inherited disease mutations resulting from IGC in ∼1% of all genes analyzed. About half of the donor sequences associated with such mutations are functional paralogous genes, suggesting that epistatic interactions or differential expression patterns will determine the impact upon fitness of specific substitutions between duplicated genes. In addition, we identified thousands of hitherto undescribed and potentially deleterious mutations that could arise via IGC. Our findings reveal the extent of the impact of interlocus gene conversion upon the spectrum of human inherited disease.
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Affiliation(s)
- Claudio Casola
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Ugne Zekonyte
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Andrew D. Phillips
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
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45
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Zhang R, Zhang L, Yu W. Genome-wide expression of non-coding RNA and global chromatin modification. Acta Biochim Biophys Sin (Shanghai) 2012; 44:40-7. [PMID: 22194012 DOI: 10.1093/abbs/gmr112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Traditionally, we know that genomic DNA will produce transcripts named messenger RNA and then translate into protein following the instruction of genetic central dogma, and RNA works here as a pass-by messenger. Now increasing evidence shows that RNA is a key regulator as well as a message transmitter. It is discovered by next-generation sequencing techniques that most genomic DNA are generally transcribed to non-coding RNA, highly beyond the percentage of coding mRNA. These non-coding RNAs (ncRNAs), belonging to several groups, have critical roles in many cellular processes, expanding our understanding of the RNA world. We review here the different categories of ncRNA according to genome location and how ncRNAs guide and recruit chromatin modification complex to specific loci of genome to modulate gene expression by affecting chromatin state.
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Affiliation(s)
- Rukui Zhang
- Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, Shanghai, China
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46
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Petronella N, Drouin G. Gene conversions in the growth hormone gene family of primates: stronger homogenizing effects in the Hominidae lineage. Genomics 2011; 98:173-81. [PMID: 21683133 DOI: 10.1016/j.ygeno.2011.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/31/2011] [Accepted: 06/01/2011] [Indexed: 11/25/2022]
Abstract
In humans, the growth hormone/chorionic somatomammotropin gene family is composed of five highly similar genes. We characterized the gene conversions that occurred between the growth hormone genes of 11 primate species. We detected 48 conversions using GENECONV and others were only detected using phylogenetic analyses. Gene conversions were detected in all species analyzed, their average size (±standard deviation) is 197.8±230.4 nucleotides, the size of the conversions is correlated with sequence similarity and converted regions are significantly more GC-rich than non-converted regions. Gene conversions have a stronger homogenizing effect in Hominidae genes than in other primate species. They are also less frequent in conserved gene regions and towards functionally important genes. This suggests that the high degree of sequence similarity observed between the growth hormone genes of primate species is a consequence of frequent gene conversions in gene regions which are under little selective constraints.
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Affiliation(s)
- Nicholas Petronella
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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47
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Tsai LP, Cheng CF, Chuang SH, Lee HH. Analysis of the CYP21A1P pseudogene: indication of mutational diversity and CYP21A2-like and duplicated CYP21A2 genes. Anal Biochem 2011; 413:133-41. [PMID: 21324303 DOI: 10.1016/j.ab.2011.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 11/16/2022]
Abstract
The CYP21A1P gene downstream of the XA gene, carrying 15 deteriorated mutations, is a nonfunctional pseudogene that shares 98% nucleotide sequence homology with CYP21A2 located on chromosome 6p21.3. However, these mutations in the CYP21A1P gene are not totally involved in each individual. From our analysis of 100 healthy ethnic Chinese (i.e., Taiwanese) (n=200 chromosomes) using the polymerase chain reaction (PCR) products combined with an amplification-created restriction site (ACRS) method and DNA sequencing, we found that approximately 10% of CYP21A1P alleles (n=195 chromosomes) presented the CYP21A2 sequence; frequencies of P30, V281, Q318, and R356 in that locus were approximately 24%, 21%, 11%, and 34%, respectively, and approximately 90% of the CYP21A1P alleles had 15 mutated loci. In addition, approximately 2.5% (n=5 chromosomes) showed four haplotypes of the 3.7-kb TaqI-produced fragment of the CYP21A2-like gene and one duplicated CYP21A2 gene. We conclude that the pseudogene of the CYP21A1P mutation presents diverse variants. Moreover, the existence of the CYP21A2-like gene is more abundant than that of the duplicated CYP21A2 gene downstream of the XA gene and could not be distinguished from the CYP21A2-TNXB gene; thus, it may be misdiagnosed by previously established methods for congenital adrenal hyperplasia caused by a 21-hydroxylase deficiency.
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Affiliation(s)
- Li-Ping Tsai
- Department of Pediatrics, Buddhist Tzu Chi General Hospital, Taipei Branch, Sindian, Taipei County 231, Taiwan
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48
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Rosengarten RD, Moreno MA, Lakkis FG, Buss LW, Dellaporta SL. Genetic diversity of the allodeterminant alr2 in Hydractinia symbiolongicarpus. Mol Biol Evol 2011; 28:933-47. [PMID: 20966116 PMCID: PMC3108555 DOI: 10.1093/molbev/msq282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hydractinia symbiolongicarpus, a colonial cnidarian (class Hydrozoa) epibiont on hermit crab shells, is well established as a model for genetic studies of allorecognition. Recently, two linked loci, allorecognition (alr) 1 and alr2, were identified by positional cloning and shown to be major determinants of histocompatibility. Both genes encode putative transmembrane proteins with hypervariable extracellular domains similar to immunoglobulin (Ig)-like domains. We sought to characterize the naturally occurring variation at the alr2 locus and to understand the origins of this molecular diversity. We examined full-length cDNA coding sequences derived from a sample of 21 field-collected colonies, including 18 chosen haphazardly and two laboratory reference strains. Of the 35 alleles recovered from the 18 unbiased samples, 34 encoded unique gene products. We identified two distinct structural classes of alleles that varied over a large central region of the gene but both possessed highly polymorphic extracellular domains I, similar to an Ig-like V-set domain. The discovery of structurally chimeric alleles provided evidence that interallelic recombination may contribute to alr2 variation. Comparisons of the genomic region encompassing alr2 from two field-derived haplotypes and one laboratory reference sequence revealed a history of structural variation at the haplotype level as well. Maintenance of large numbers of equally rare alleles in a natural population is a hallmark of negative frequency-dependent selection and is expected to produce high levels of heterozygosity. The observed alr2 allelic diversity is comparable with that found in immune recognition molecules such as human leukocyte antigens, B cell Igs, or natural killer cell Ig-like receptors.
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Affiliation(s)
- Rafael D Rosengarten
- Department of Molecular, Cellular and Developmental Biology, Yale University, Yale, CN, USA.
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Advances in Research on Pseudogenes. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Khurana E, Lam HYK, Cheng C, Carriero N, Cayting P, Gerstein MB. Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic Acids Res 2010; 38:6997-7007. [PMID: 20615899 PMCID: PMC2978362 DOI: 10.1093/nar/gkq587] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Duplicated pseudogenes in the human genome are disabled copies of functioning parent genes. They result from block duplication events occurring throughout evolutionary history. Relatively recent duplications (with sequence similarity ≥90% and length ≥1 kb) are termed segmental duplications (SDs); here, we analyze the interrelationship of SDs and pseudogenes. We present a decision-tree approach to classify pseudogenes based on their (and their parents’) characteristics in relation to SDs. The classification identifies 140 novel pseudogenes and makes possible improved annotation for the 3172 pseudogenes located in SDs. In particular, it reveals that many pseudogenes in SDs likely did not arise directly from parent genes, but are the result of a multi-step process. In these cases, the initial duplication or retrotransposition of a parent gene gives rise to a ‘parent pseudogene’, followed by further duplication creating duplicated–duplicated or duplicated–processed pseudogenes, respectively. Moreover, we can precisely identify these parent pseudogenes by overlap with ancestral SD loci. Finally, a comparison of nucleotide substitutions per site in a pseudogene with its surrounding SD region allows us to estimate the time difference between duplication and disablement events, and this suggests that most duplicated pseudogenes in SDs were likely disabled around the time of the original duplication.
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Affiliation(s)
- Ekta Khurana
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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