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Li L, Jia C, Tang Y, Kong Y, Xia Y, Ma L. Novel Gross Deletion Mutations in NTRK1 Gene Associated With Congenital Insensitivity to Pain With Anhidrosis. Front Pediatr 2021; 9:638190. [PMID: 33748046 PMCID: PMC7969531 DOI: 10.3389/fped.2021.638190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Congenital insensitivity to pain with anhidrosis (CIPA) is a rare inherited autosomal recessive disorder characterized by insensitivity to noxious stimuli, anhidrosis, recurrent fever, and intellectual disability. CIPA is mainly caused by mutations in the neurotrophic tyrosine kinase receptor type 1 gene (NTRK1). This study aims to identify pathogenic mutations underlying CIPA in two unrelated Chinese families. Methods: DNA was extracted from blood samples of patients and their available family members and subjected to whole exome sequencing (WES). Real-time PCR (qPCR), Gap-PCR, and Sanger sequencing were applied to verify the identified variants. Result: We found novel compound gross deletion mutations [exon1-6 del (g.1-1258_10169del); exon5-7 del (g.6995_11999del)] of NTRK1 (MIM 191315) gene in family 1 and the compound heterozygous mutations [c.851-33T>A; exon5-7 del (g.6995_11999del)] in family 2. Interestingly, we discovered the intragenic novel gross deletion [exon5-7 del (g.6995_11999del)] mediated by recombination between Alu elements. Conclusions: The present study highlights two rare gross deletion mutations in the NTRK1 gene associated with CIPA in two unrelated Chinese families. The deletion of exon1-6 (g.1-1258_10169del) is thought to be the largest NTRK1 deletion reported to date. Our findings expand the mutation spectrum of NTRK1 mutations in the Chinese and could be useful for prenatal interventions and more precise pharmacological treatments to patients. WES conducted in our study is a convenient and useful tool for clinical diagnosis of CIPA and other associated disorders.
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Affiliation(s)
- Lulu Li
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Chao Jia
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
| | - Yue Tang
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yuanyuan Kong
- Department of Newborn Screening Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yaofang Xia
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
| | - Li Ma
- Department of Neonatology, Hebei Provincial Children's Hospital, Shijiazhuang, China
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Li S, Zong L, Hou Y, Zhang W, Zhou L, Yang Q, Wang L, Jiang W, Li Q, Huang X, Ning Y, Wen Z, Zhao C. Altered DNA methylation of the AluY subfamily in schizophrenia and bipolar disorder. Epigenomics 2019; 11:581-586. [PMID: 31066577 DOI: 10.2217/epi-2018-0139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To study DNA methylation patterns of AluY subfamilies in schizophrenia (SCZ) and bipolar disorder (BPD). Patients & methods: A bisulfite conversion-specific one-label extension method was employed to detect the AluY subfamily methylation levels of peripheral blood DNA from 92 SCZ patients, 99 BPD patients and 92 controls. Results: Hypermethylation of the AluY A1 and A2 CpG sites in BPD patients and hypomethylation of A3 CpG site in both of BPD and SCZ patients, and opposite age-dependent methylation alterations between SCZ and controls. Conclusion: The differentially altered DNA methylation patterns of the AluY families between BPD and SCZ suggest the role of DNA methylation in the pathogenesis of these major psychiatric disorders.
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Affiliation(s)
- Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology & Application, and Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China
| | - Lu Zong
- Center for Reproductive Medicine, The First Affiliated Hospital of University of Science & Technology of China, Hefei, Anhui, China
| | - Yu Hou
- Department of Pediatric Neurology, Affiliated BaYi Children's Hospital, PLA Army General Hospital, Beijing, China
| | - Wenwei Zhang
- Department of Psychiatry, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Lin Zhou
- Key Laboratory of Genetics & Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, China
| | - Qiong Yang
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Lijuan Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology & Application, and Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China
| | - Wei Jiang
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology & Application, and Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiyang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology & Application, and Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingbing Huang
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Yuping Ning
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Zhexing Wen
- Departments of Psychiatry and Behavior Sciences, Cell Biology, and Neurology, Emory University, Atlanta, GA, USA
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Guangdong Provincial Key Laboratory of Single Cell Technology & Application, and Key Laboratory of Mental Health of the Ministry of Education, Southern Medical University, Guangzhou, Guangdong, China
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Identification of Alternative Variants and Insertion of the Novel Polymorphic AluYl17 in TSEN54 Gene during Primate Evolution. Int J Genomics 2016; 2016:1679574. [PMID: 28083540 PMCID: PMC5204098 DOI: 10.1155/2016/1679574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/30/2016] [Indexed: 11/24/2022] Open
Abstract
TSEN54 encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified an AluSx-derived alternative transcript in TSEN54 of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR) amplification and TSEN54 sequence analysis of primate and human samples identified five novel alternative transcripts, including the AluSx exonized transcript. Additionally, we performed comparative expression analysis via RT-qPCR in various cynomolgus, rhesus monkey, and human tissues. RT-qPCR amplification revealed differential expression patterns. Furthermore, genomic PCR amplification and sequencing of primate and human DNA samples revealed that AluSx elements were integrated in human and all of the primate samples tested. Intriguingly, in langur genomic DNA, an additional AluY element was inserted into AluSx of intron eight of TSEN54. The new AluY element showed polymorphic insertion. Using standardized nomenclature for Alu repeats, the polymorphic AluY of the langur TSEN54 was designated as being of the AluYl17 subfamily. Our results suggest that integration of the AluSx element in TSEN54 contributed to diversity in transcripts and induced lineage- or species-specific evolutionary events such as alternative splicing and polymorphic insertion during primate evolution.
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Teixeira-Silva A, Silva RM, Carneiro J, Amorim A, Azevedo L. The role of recombination in the origin and evolution of Alu subfamilies. PLoS One 2013; 8:e64884. [PMID: 23750218 PMCID: PMC3672193 DOI: 10.1371/journal.pone.0064884] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/19/2013] [Indexed: 01/25/2023] Open
Abstract
Alus are the most abundant and successful short interspersed nuclear elements found in primate genomes. In humans, they represent about 10% of the genome, although few are retrotransposition-competent and are clustered into subfamilies according to the source gene from which they evolved. Recombination between them can lead to genomic rearrangements of clinical and evolutionary significance. In this study, we have addressed the role of recombination in the origin of chimeric Alu source genes by the analysis of all known consensus sequences of human Alus. From the allelic diversity of Alu consensus sequences, validated in extant elements resulting from whole genome searches, distinct events of recombination were detected in the origin of particular subfamilies of AluS and AluY source genes. These results demonstrate that at least two subfamilies are likely to have emerged from ectopic Alu-Alu recombination, which stimulates further research regarding the potential of chimeric active Alus to punctuate the genome.
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Affiliation(s)
- Ana Teixeira-Silva
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Raquel M. Silva
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - João Carneiro
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - António Amorim
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FCUP-Faculty of Sciences, University of Porto, Porto, Portugal
| | - Luísa Azevedo
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- * E-mail:
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Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GKK, Ng HK, Zhang L, Xue H. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome. BMC Genomics 2011; 12:564. [PMID: 22087792 PMCID: PMC3228862 DOI: 10.1186/1471-2164-12-564] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 11/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. RESULTS Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. CONCLUSIONS AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.
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Affiliation(s)
- Lingling Mei
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, 1 University Road, Clear Water Bay, Kowloon, Hong Kong, China.
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Bochukova EG, Roscioli T, Hedges DJ, Taylor IB, Johnson D, David DJ, Deininger PL, Wilkie AO. Rare mutations ofFGFR2causing apert syndrome: identification of the first partial gene deletion, and anAluelement insertion from a new subfamily. Hum Mutat 2009; 30:204-11. [DOI: 10.1002/humu.20825] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Salih F, Salih B, Kogan S, Trifonov EN. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J Biomol Struct Dyn 2008; 26:9-16. [PMID: 18533722 DOI: 10.1080/07391102.2008.10507219] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Alu sequences carry periodical pattern with CG dinucleotides (CpG) repeating every 31-32 bases. Similar distances are observed in distribution of DNA curvature in crystallized nucleosomes, at positions +/-1.5 and +/-4.5 periods of DNA from nucleosome DNA dyad. Since CG elements are also found to impart to nucleosomes higher stability when positioned at +/-1.5 sites, it suggests that CG dinucleotides may play a role in modulation of the nucleosome strength when the CG elements are methylated. Thus, Alu sequences may harbor special epigenetic nucleosomes with methylation-dependent regulatory functions. Nucleosome DNA sequence probe is suggested to detect locations of such regulatory nucleosomes in the sequences.
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Affiliation(s)
- F Salih
- Genome Diversity Center, Institute of Evolution, University of Haifa, Israel
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Identification and characterisation of a large senataxin (SETX) gene duplication in ataxia with ocular apraxia type 2 (AOA2). Neurogenetics 2008; 9:295-9. [PMID: 18663494 DOI: 10.1007/s10048-008-0139-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/10/2008] [Indexed: 10/21/2022]
Abstract
Autosomal recessive cerebellar ataxia with ocular apraxia type 2 (AOA2) is a neurodegenerative disorder characterised by early onset cerebellar ataxia, sensory-motor neuropathy and frequently increased levels of alpha-fetoprotein. We describe a male patient with a phenotype highly suggestive of AOA2, but only one point mutation found by sequencing of the SETX gene. Further analysis revealed a large out-of-frame tandem duplication, encompassing exons 7, 8, 9 and 10. This duplication event occurred obviously by unequal homologous recombination between AluY sequences. Gross SETX deletions or duplications might be an underestimated cause of AOA2.
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Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet 2007; 23:183-91. [PMID: 17331616 DOI: 10.1016/j.tig.2007.02.006] [Citation(s) in RCA: 322] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 01/15/2007] [Accepted: 02/12/2007] [Indexed: 01/20/2023]
Abstract
Although a large proportion (44%) of the human genome is occupied by transposons and transposon-like repetitive elements, only a small proportion (<0.05%) of these elements remain active today. Recent evidence indicates that approximately 35-40 subfamilies of Alu, L1 and SVA elements (and possibly HERV-K elements) remain actively mobile in the human genome. These active transposons are of great interest because they continue to produce genetic diversity in human populations and also cause human diseases by integrating into genes. In this review, we examine these active human transposons and explore mechanistic factors that influence their mobilization.
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Affiliation(s)
- Ryan E Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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