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Kozłowska-Masłoń J, Ciomborowska-Basheer J, Kubiak MR, Makałowska I. Evolution of retrocopies in the context of HUSH silencing. Biol Direct 2024; 19:60. [PMID: 39095906 PMCID: PMC11295320 DOI: 10.1186/s13062-024-00507-9] [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: 04/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Retrotransposition is one of the main factors responsible for gene duplication and thus genome evolution. However, the sequences that undergo this process are not only an excellent source of biological diversity, but in certain cases also pose a threat to the integrity of the DNA. One of the mechanisms that protects against the incorporation of mobile elements is the HUSH complex, which is responsible for silencing long, intronless, transcriptionally active transposed sequences that are rich in adenine on the sense strand. In this study, broad sets of human and porcine retrocopies were analysed with respect to the above factors, taking into account evolution of these molecules. Analysis of expression pattern, genomic structure, transcript length, and nucleotide substitution frequency showed the strong relationship between the expression level and exon length as well as the protective nature of introns. The results of the studies also showed that there is no direct correlation between the expression level and adenine content. However, protein-coding retrocopies, which have a lower adenine content, have a significantly higher expression level than the adenine-rich non-coding but expressed retrocopies. Therefore, although the mechanism of HUSH silencing may be an important part of the regulation of retrocopy expression, it is one component of a more complex molecular network that remains to be elucidated.
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Affiliation(s)
- Joanna Kozłowska-Masłoń
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, Poznań, Poland
| | - Joanna Ciomborowska-Basheer
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
- Laboratory of Nature Education and Conservation, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magdalena Regina Kubiak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland.
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Borovská I, Vořechovský I, Královičová J. Alu RNA fold links splicing with signal recognition particle proteins. Nucleic Acids Res 2023; 51:8199-8216. [PMID: 37309897 PMCID: PMC10450188 DOI: 10.1093/nar/gkad500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
Transcriptomic diversity in primates was considerably expanded by exonizations of intronic Alu elements. To better understand their cellular mechanisms we have used structure-based mutagenesis coupled with functional and proteomic assays to study the impact of successive primate mutations and their combinations on inclusion of a sense-oriented AluJ exon in the human F8 gene. We show that the splicing outcome was better predicted by consecutive RNA conformation changes than by computationally derived splicing regulatory motifs. We also demonstrate an involvement of SRP9/14 (signal recognition particle) heterodimer in splicing regulation of Alu-derived exons. Nucleotide substitutions that accumulated during primate evolution relaxed the conserved left-arm AluJ structure including helix H1 and reduced the capacity of SRP9/14 to stabilize the closed Alu conformation. RNA secondary structure-constrained mutations that promoted open Y-shaped conformations of the Alu made the Alu exon inclusion reliant on DHX9. Finally, we identified additional SRP9/14 sensitive Alu exons and predicted their functional roles in the cell. Together, these results provide unique insights into architectural elements required for sense Alu exonization, identify conserved pre-mRNA structures involved in exon selection and point to a possible chaperone activity of SRP9/14 outside the mammalian signal recognition particle.
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Affiliation(s)
- Ivana Borovská
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
| | - Igor Vořechovský
- Faculty of Medicine, University of Southampton, HDH, MP808, Southampton SO16 6YD, United Kingdom
| | - Jana Královičová
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Bratislava 840 05, Slovak Republic
- Institute of Zoology, Slovak Academy of Sciences, Bratislava 845 06, Slovak Republic
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Wang J, Weatheritt R, Voineagu I. Alu-minating the Mechanisms Underlying Primate Cortex Evolution. Biol Psychiatry 2022; 92:760-771. [PMID: 35981906 DOI: 10.1016/j.biopsych.2022.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 11/02/2022]
Abstract
The higher-order cognitive functions observed in primates correlate with the evolutionary enhancement of cortical volume and folding, which in turn are driven by the primate-specific expansion of cellular diversity in the developing cortex. Underlying these changes is the diversification of molecular features including the creation of human and/or primate-specific genes, the activation of specific molecular pathways, and the interplay of diverse layers of gene regulation. We review and discuss evidence for connections between Alu elements and primate brain evolution, the evolutionary milestones of which are known to coincide along primate lineages. Alus are repetitive elements that contribute extensively to the acquisition of novel genes and the expansion of diverse gene regulatory layers, including enhancers, alternative splicing, RNA editing, and microRNA pathways. By reviewing the impact of Alus on molecular features linked to cortical expansions or gyrification or implications in cognitive deficits, we suggest that future research focusing on the role of Alu-derived molecular events in the context of brain development may greatly advance our understanding of higher-order cognitive functions and neurologic disorders.
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Affiliation(s)
- Juli Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.
| | - Robert Weatheritt
- St Vincent Clinical School, University of New South Wales, Sydney, Australia; Garvan Institute of Medical Research, EMBL Australia, Sydney, New South Wales, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Cellular Genomics Futures Institute, University of New South Wales, Sydney, Australia.
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Peng C, Niu L, Deng J, Yu J, Zhang X, Zhou C, Xing J, Li J. Can-SINE dynamics in the giant panda and three other Caniformia genomes. Mob DNA 2018; 9:32. [PMID: 30455747 PMCID: PMC6230240 DOI: 10.1186/s13100-018-0137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.
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Affiliation(s)
- Changjun Peng
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Lili Niu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jianqiu Yu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Xueyan Zhang
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Chuang Zhou
- 3Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan China
| | - Jinchuan Xing
- 4Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Jing Li
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
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Nakama M, Otsuka H, Ago Y, Sasai H, Abdelkreem E, Aoyama Y, Fukao T. Intronic antisense Alu elements have a negative splicing effect on the inclusion of adjacent downstream exons. Gene 2018; 664:84-89. [PMID: 29698748 DOI: 10.1016/j.gene.2018.04.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/05/2018] [Accepted: 04/20/2018] [Indexed: 02/08/2023]
Abstract
Alu elements occupy 10% of the human genome. However, although they contribute to genomic and transcriptomic diversity, their function is still not fully understood. We hypothesized that intronic Alu elements may contribute to alternative splicing. We therefore examined their effect on splicing using minigene constructs including exon 9-exon 11 inclusive of ACAT1 with truncated introns 9 and 10. These constructs contained a suboptimal splice acceptor site for intron 9. Insertion of AluY-partial AluSz6-AluSx, originally located in ACAT1 intron 5, in an antisense direction within intron 9 had a negative effect on exon 10 inclusion. This effect was additive with that of an exonic splicing enhancer mutation in exon 10, and was canceled by the substitution of G for C at the first nucleotide of exon 10 which optimized the splice acceptor site of intron 9. A sense AluY-partial AluSz6-AluSx insertion had no effect on exon 10 inclusion, and one antisense AluSx insertion had a similar effect to antisense AluY-partial AluSz6-AluSx insertion. The shorter the distance between the antisense Alu element and exon 10, the greater the negative effect on exon 10 inclusion. This distance effect was more evident for suboptimal than optimal splice sites. Based on our data, we propose that intronic antisense Alu elements contribute to alternative splicing and transcriptomic diversity in some genes, especially when splice acceptor sites are suboptimal.
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Affiliation(s)
- Mina Nakama
- Division of Clinical Genetics, Gifu University Hospital, Gifu, Japan; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Otsuka
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Yasuhiko Ago
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hideo Sasai
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Elsayed Abdelkreem
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Department of Pediatrics, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Yuka Aoyama
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Kasugai, Japan
| | - Toshiyuki Fukao
- Division of Clinical Genetics, Gifu University Hospital, Gifu, Japan; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan.
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6
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Saeliw T, Tangsuwansri C, Thongkorn S, Chonchaiya W, Suphapeetiporn K, Mutirangura A, Tencomnao T, Hu VW, Sarachana T. Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder. Mol Autism 2018; 9:27. [PMID: 29686828 PMCID: PMC5902935 DOI: 10.1186/s13229-018-0213-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Background Alu elements are a group of repetitive elements that can influence gene expression through CpG residues and transcription factor binding. Altered gene expression and methylation profiles have been reported in various tissues and cell lines from individuals with autism spectrum disorder (ASD). However, the role of Alu elements in ASD remains unclear. We thus investigated whether Alu elements are associated with altered gene expression profiles in ASD. Methods We obtained five blood-based gene expression profiles from the Gene Expression Omnibus database and human Alu-inserted gene lists from the TranspoGene database. Differentially expressed genes (DEGs) in ASD were identified from each study and overlapped with the human Alu-inserted genes. The biological functions and networks of Alu-inserted DEGs were then predicted by Ingenuity Pathway Analysis (IPA). A combined bisulfite restriction analysis of lymphoblastoid cell lines (LCLs) derived from 36 ASD and 20 sex- and age-matched unaffected individuals was performed to assess the global DNA methylation levels within Alu elements, and the Alu expression levels were determined by quantitative RT-PCR. Results In ASD blood or blood-derived cells, 320 Alu-inserted genes were reproducibly differentially expressed. Biological function and pathway analysis showed that these genes were significantly associated with neurodevelopmental disorders and neurological functions involved in ASD etiology. Interestingly, estrogen receptor and androgen signaling pathways implicated in the sex bias of ASD, as well as IL-6 signaling and neuroinflammation signaling pathways, were also highlighted. Alu methylation was not significantly different between the ASD and sex- and age-matched control groups. However, significantly altered Alu methylation patterns were observed in ASD cases sub-grouped based on Autism Diagnostic Interview-Revised scores compared with matched controls. Quantitative RT-PCR analysis of Alu expression also showed significant differences between ASD subgroups. Interestingly, Alu expression was correlated with methylation status in one phenotypic ASD subgroup. Conclusion Alu methylation and expression were altered in LCLs from ASD subgroups. Our findings highlight the association of Alu elements with gene dysregulation in ASD blood samples and warrant further investigation. Moreover, the classification of ASD individuals into subgroups based on phenotypes may be beneficial and could provide insights into the still unknown etiology and the underlying mechanisms of ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0213-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thanit Saeliw
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chayanin Tangsuwansri
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Surangrat Thongkorn
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Weerasak Chonchaiya
- 2Maximizing Thai Children's Developmental Potential Research Unit, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- 3Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Apiwat Mutirangura
- 5Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- 6Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand
| | - Valerie W Hu
- 7Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, The George Washington University, Washington, DC USA
| | - Tewarit Sarachana
- 6Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand
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7
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Lavi E, Carmel L. Alu exaptation enriches the human transcriptome by introducing new gene ends. RNA Biol 2018; 15:715-725. [PMID: 29493382 DOI: 10.1080/15476286.2018.1429880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal. We therefore studied what evolutionary processes might explain the formation of these specific hotspots of novel gene ends. We show that two of the three hotspots might have emerged from mutational processes that turned sequences that resemble polyadenylation signals into full-blown canonical signals, whereas one hotspot is tightly linked to the process of Alu insertion into the genome. Overall, Alu elements may lie behind the formation of 302 new gene end variants, affecting a total of 243 genes. Intergenic Alu elements may elongate genes by creating a downstream cleavage site, intronic Alu elements may lead to gene variants which code for truncated proteins, and 3'UTR Alu elements may result in gene variants with alternative 3'UTR.
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Affiliation(s)
- Eitan Lavi
- a Department of Genetics , The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem , Israel
| | - Liran Carmel
- a Department of Genetics , The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem , Israel
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8
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Daskalova E, Baev V, Rusinov V, Minkov I. 3'UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent research data reveal complex, network-based interactions between mobile elements and regulatory systems of eukaryotic cells. In this article, we focus on regulatory interactions between Alu elements and micro RNAs (miRNAs). Our results show that the majority of the Alu sequences inserted in 3'UTRs of analyzed human genes carry strong potential target sites for at least 53 different miRNAs. Thus, 3'UTR-located Alu elements may play the role of mobile regulatory modules that supply binding sites for miRNA regulation. Their abundance and ability to distribute a set of certain miRNA target sites may have an important role in establishment, extension, network organization, and, as we suppose – in the regulation and environment-dependent activation/inactivation of some elements of the miRNA regulatory system, as well as for a larger scale RNA-based regulatory interactions. The Alu-miRNA connection may be crucial especially for the primate/human evolution.
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Affiliation(s)
- Evelina Daskalova
- University of Plovdiv, Department of Plant Physiology and Molecular Biology, 24, Tsar Assen St., 4000 Plovdiv, Bulgaria
| | - Vesselin Baev
- University of Plovdiv, Department of Plant Physiology and Molecular Biology, 24, Tsar Assen St., 4000 Plovdiv, Bulgaria
| | - Ventsislav Rusinov
- University of Plovdiv, Department of Plant Physiology and Molecular Biology, 24, Tsar Assen St., 4000 Plovdiv, Bulgaria
| | - Ivan Minkov
- University of Plovdiv, Department of Plant Physiology and Molecular Biology, 24, Tsar Assen St., 4000 Plovdiv, Bulgaria
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9
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Pease LI, Clegg PD, Proctor CJ, Shanley DJ, Cockell SJ, Peffers MJ. Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females. Sci Rep 2017; 7:14443. [PMID: 29089527 PMCID: PMC5663855 DOI: 10.1038/s41598-017-14650-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/13/2017] [Indexed: 01/21/2023] Open
Abstract
The development of tendinopathy is influenced by a variety of factors including age, gender, sex hormones and diabetes status. Cross platform comparative analysis of transcriptomic data elucidated the connections between these entities in the context of ageing. Tissue-engineered tendons differentiated from bone marrow derived mesenchymal stem cells from young (20-24 years) and old (54-70 years) donors were assayed using ribonucleic acid sequencing (RNA-seq). Extension of the experiment to microarray and RNA-seq data from tendon identified gender specific gene expression changes highlighting disparity with existing literature and published pathways. Separation of RNA-seq data by sex revealed underlying negative binomial distributions which increased statistical power. Sex specific de novo transcriptome assemblies generated fewer larger transcripts that contained miRNAs, lincRNAs and snoRNAs. The results identify that in old males decreased expression of CRABP2 leads to cell proliferation, whereas in old females it leads to cellular senescence. In conjunction with existing literature the results explain gender disparity in the development and types of degenerative diseases as well as highlighting a wide range of considerations for the analysis of transcriptomic data. Wider implications are that degenerative diseases may need to be treated differently in males and females because alternative mechanisms may be involved.
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Affiliation(s)
- Louise I Pease
- MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
| | - Peter D Clegg
- MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, The University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Carole J Proctor
- MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK
| | - Daryl J Shanley
- MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, NE1 7RU, UK
| | - Simon J Cockell
- Faculty of Medical Sciences, Bioinformatics Support Unit, Framlington Place, Newcastle University, Newcastle, NE2 4HH, UK
| | - Mandy J Peffers
- MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA), Liverpool, UK.
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, The University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK.
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10
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Baker JN, Walker JA, Vanchiere JA, Phillippe KR, St. Romain CP, Gonzalez-Quiroga P, Denham MW, Mierl JR, Konkel MK, Batzer MA. Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. Genome Biol Evol 2017; 9:2365-2376. [PMID: 28957461 PMCID: PMC5622375 DOI: 10.1093/gbe/evx172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2017] [Indexed: 12/22/2022] Open
Abstract
Squirrel monkeys, Saimiri, are commonly found in zoological parks and used in biomedical research. S. boliviensis is the most common species for research; however, there is little information about genome evolution within this primate lineage. Here, we reconstruct the Alu element sequence amplification and evolution in the genus Saimiri at the time of divergence within the family Cebidae lineage. Alu elements are the most successful SINE (Short Interspersed Element) in primates. Here, we report 46 Saimiri lineage specific Alu subfamilies. Retrotransposition activity involved subfamilies related to AluS, AluTa10, and AluTa15. Many subfamilies are simultaneously active within the Saimiri lineage, a finding which supports the stealth model of Alu amplification. We also report a high resolution analysis of Alu subfamilies within the S. boliviensis genome [saiBol1].
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Affiliation(s)
- Jasmine N. Baker
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - John A. Vanchiere
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport
| | - Kacie R. Phillippe
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | | | | | - Michael W. Denham
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Jackson R. Mierl
- Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Miriam K. Konkel
- Department of Biological Sciences, Louisiana State University, Baton Rouge
- Department of Biological Sciences, Clemson University, South Carolina
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge
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11
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Narváez DM, Groot H, Diaz SM, Palma RM, Muñoz N, Cros MP, Hernández-Vargas H. Oxidative stress and repetitive element methylation changes in artisanal gold miners occupationally exposed to mercury. Heliyon 2017; 3:e00400. [PMID: 28948237 PMCID: PMC5602780 DOI: 10.1016/j.heliyon.2017.e00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/08/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022] Open
Abstract
Mercury (Hg) exposure is a public health concern due to its persistence in the environment and its high toxicity. Such toxicity has been associated with the generation of oxidative stress in occupationally exposed subjects, such as artisanal gold miners. In this study, we characterize occupational exposure to Hg by measuring blood, urine and hair levels, and investigate oxidative stress and DNA methylation associated with gold mining. To do this, samples from 53 miners and 36 controls were assessed. We show higher levels of oxidative stress marker 8-OHdG in the miners. Differences in LINE1 and Alu(Yb8) DNA methylation between gold miners and control group are present in peripheral blood leukocytes. LINE1 methylation is positively correlated with 8-OHdG levels, while XRCC1 and LINE1 methylation are positively correlated with Hg levels. These results suggest an effect of Hg on oxidative stress and DNA methylation in gold miners that may have an impact on miners' health.
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Affiliation(s)
- Diana M. Narváez
- Human Genetics Laboratory. Universidad de los Andes. Bogotá, Colombia
- Instituto Nacional de Salud (INS). Bogotá, Colombia
- Epigenetics Group. International Agency for Research on Cancer (IARC). Lyon, France
| | - Helena Groot
- Human Genetics Laboratory. Universidad de los Andes. Bogotá, Colombia
| | | | | | | | - Marie-Pierre Cros
- Epigenetics Group. International Agency for Research on Cancer (IARC). Lyon, France
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12
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Feusier J, Witherspoon DJ, Scott Watkins W, Goubert C, Sasani TA, Jorde LB. Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. Mob DNA 2017; 8:9. [PMID: 28770012 PMCID: PMC5531096 DOI: 10.1186/s13100-017-0093-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements. Combining multiple discovery approaches may provide a better profile of the polymorphic Alu mobilome. AluYb8/9 elements have been a focus of our recent studies as they are young subfamilies (~2.3 million years old) that contribute ~30% of recent polymorphic Alu retrotransposition events. Here, we update our ME-Scan methods for detecting Alu elements and apply these methods to discover new insertions in a large set of individuals with diverse ancestral backgrounds. RESULTS We identified 5,288 putative Alu insertion events, including several hundred novel AluYb8/9 elements from 213 individuals from 18 diverse human populations. Hundreds of these loci were specific to continental populations, and 23 non-reference population-specific loci were validated by PCR. We provide high-quality sequence information for 68 rare AluYb8/9 elements, of which 11 have hallmarks of an active source element. Our subfamily distribution of rare AluYb8/9 elements is consistent with previous datasets, and may be representative of rare loci. We also find that while ME-Scan and low-coverage, whole-genome sequencing (WGS) detect different Alu elements in 41 1000 Genomes individuals, the two methods yield similar population structure results. CONCLUSION Current in-silico methods for Alu discovery may miss rare, polymorphic Alu elements. Therefore, using multiple techniques can provide a more accurate profile of Alu elements in individuals and populations. We improved our false-negative rate as an indicator of sample quality for future ME-Scan experiments. In conclusion, we demonstrate that ME-Scan is a good supplement for next-generation sequencing methods and is well-suited for population-level analyses.
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Affiliation(s)
- Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - W. Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Clément Goubert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Thomas A. Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
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Kryatova MS, Steranka JP, Burns KH, Payer LM. Insertion and deletion polymorphisms of the ancient AluS family in the human genome. Mob DNA 2017; 8:6. [PMID: 28450901 PMCID: PMC5402677 DOI: 10.1186/s13100-017-0089-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/04/2017] [Indexed: 01/09/2023] Open
Abstract
Background Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome. Results Of 52 previously reported polymorphic AluS elements ascertained for this study, 48 were confirmed to belong to the AluS subfamily using high stringency subfamily classification criteria. Of these, the majority (77%, 37/48) appear to be deletion polymorphisms. Two polymorphic AluS elements (4%) have features of non-classical Alu insertions and one polymorphic AluS element (2%) likely inserted by a mechanism involving internal priming. Seven AluS polymorphisms (15%) appear to have arisen by the classical target-primed reverse transcription (TPRT) retrotransposition mechanism. These seven TPRT products are 3′ intact with 3′ poly-A tails, and are flanked by target site duplications; L1 ORF2p endonuclease cleavage sites were also observed, providing additional evidence that these are L1 ORF2p endonuclease-mediated TPRT insertions. Further sequence analysis showed strong conservation of both the RNA polymerase III promoter and SRP9/14 binding sites, important for mediating transcription and interaction with retrotransposition machinery, respectively. This conservation of functional features implies that some of these are fairly recent insertions since they have not diverged significantly from their respective retrotranspositionally competent source elements. Conclusions Of the polymorphic AluS elements evaluated in this report, 15% (7/48) have features consistent with TPRT-mediated insertion, thus suggesting that some AluS elements have been more active recently than previously thought, or that fixation of AluS insertion alleles remains incomplete. These data expand the potential significance of polymorphic AluS elements in contributing to structural variation in the human genome. Future discovery efforts focusing on polymorphic AluS elements are likely to identify more such polymorphisms, and approaches tailored to identify deletion alleles may be warranted. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0089-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria S Kryatova
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
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Neurotoxic Doses of Chronic Methamphetamine Trigger Retrotransposition of the Identifier Element in Rat Dorsal Dentate Gyrus. Genes (Basel) 2017; 8:genes8030096. [PMID: 28272323 PMCID: PMC5368700 DOI: 10.3390/genes8030096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
Short interspersed elements (SINEs) are typically silenced by DNA hypermethylation in somatic cells, but can retrotranspose in proliferating cells during adult neurogenesis. Hypomethylation caused by disease pathology or genotoxic stress leads to genomic instability of SINEs. The goal of the present investigation was to determine whether neurotoxic doses of binge or chronic methamphetamine (METH) trigger retrotransposition of the identifier (ID) element, a member of the rat SINE family, in the dentate gyrus genomic DNA. Adult male Sprague-Dawley rats were treated with saline or high doses of binge or chronic METH and sacrificed at three different time points thereafter. DNA methylation analysis, immunohistochemistry and next-generation sequencing (NGS) were performed on the dorsal dentate gyrus samples. Binge METH triggered hypomethylation, while chronic METH triggered hypermethylation of the CpG-2 site. Both METH regimens were associated with increased intensities in poly(A)-binding protein 1 (PABP1, a SINE regulatory protein)-like immunohistochemical staining in the dentate gyrus. The amplification of several ID element sequences was significantly higher in the chronic METH group than in the control group a week after METH, and they mapped to genes coding for proteins regulating cell growth and proliferation, transcription, protein function as well as for a variety of transporters. The results suggest that chronic METH induces ID element retrotransposition in the dorsal dentate gyrus and may affect hippocampal neurogenesis.
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15
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Sheinman M, Ramisch A, Massip F, Arndt PF. Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences. Sci Rep 2016; 6:30851. [PMID: 27488939 PMCID: PMC4973250 DOI: 10.1038/srep30851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 12/26/2022] Open
Abstract
Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf's law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes.
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Affiliation(s)
- Michael Sheinman
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Anna Ramisch
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Florian Massip
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- INRA, UR1404 Mathématique Informatique Appliquées du Génome á l’Environnement-F-78350 Jouy-en Josas, France
| | - Peter F. Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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16
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Platt RN, Mangum SF, Ray DA. Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. Mob DNA 2016; 7:12. [PMID: 27489570 PMCID: PMC4971623 DOI: 10.1186/s13100-016-0071-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/13/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Around 40 million years ago DNA transposons began accumulating in an ancestor of bats in the family Vespertilionidae. Since that time, Class II transposons have been continuously reinvading and accumulating in vespertilionid genomes at a rate that is unprecedented in mammals. Miniopterus (Miniopteridae), a genus of long-fingered bats that was recently elevated from Vespertilionidae, is the sister taxon to the vespertilionids and is often used as an outgroup when studying transposable elements in vesper bats. Previous wet-lab techniques failed to identify Helitrons, TcMariners, or hAT transposons in Miniopterus. Limitations of those methods and ambiguous results regarding the distribution of piggyBac transposons left some questions as to the distribution of Class II elements in this group. The recent release of the Miniopterus natalensis genome allows for transposable element discovery with a higher degree of precision. RESULTS Here we analyze the transposable element content of M. natalensis to pinpoint with greater accuracy the taxonomic distribution of Class II transposable elements in bats. These efforts demonstrate that, compared to the vespertilionids, Class II TEs are highly mutated and comprise only a small portion of the M. natalensis genome. Despite the limited Class II content, M. natalensis possesses a limited number of lineage-specific, low copy number piggyBacs and shares several TcMariner families with vespertilionid bats. Multiple efforts to identify Helitrons, one of the major TE components of vesper bat genomes, using de novo repeat identification and structural based searches failed. CONCLUSIONS These observations combined with previous results inform our understanding of the events leading to the unique Class II element acquisition that characterizes vespertilionids. While it appears that a small number of TcMariner and piggyBac elements were deposited in the ancestral Miniopterus + vespertilionid genome, these elements are not present in M. natalensis genome at high copy number. Instead, this work indicates that the vesper bats alone experienced the expansion of TEs ranging from Helitrons to piggyBacs to hATs.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
| | - Sarah F Mangum
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX 79409-3131 USA
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17
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Faulk C, Kim JH, Anderson OS, Nahar MS, Jones TR, Sartor MA, Dolinoy DC. Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A. Epigenetics 2016; 11:489-500. [PMID: 27267941 PMCID: PMC4939917 DOI: 10.1080/15592294.2016.1183856] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Developmental exposure to bisphenol A (BPA) has been shown to induce changes in DNA methylation in both mouse and human genic regions; however, the response in repetitive elements and transposons has not been explored. Here we present novel methodology to combine genomic DNA enrichment with RepeatMasker analysis on next-generation sequencing data to determine the effect of perinatal BPA exposure on repetitive DNA at the class, family, subfamily, and individual insertion level in both mouse and human samples. Mice were treated during gestation and lactation to BPA in chow at 0, 50, or 50,000 ng/g levels and total BPA was measured in stratified human fetal liver tissue samples as low (non-detect to 0.83 ng/g), medium (3.5 to 5.79 ng/g), or high (35.44 to 96.76 ng/g). Transposon methylation changes were evident in human classes, families, and subfamilies, with the medium group exhibiting hypomethylation compared to both high and low BPA groups. Mouse repeat classes, families, and subfamilies did not respond to BPA with significantly detectable differential DNA methylation. In human samples, 1251 individual transposon loci were detected as differentially methylated by BPA exposure, but only 19 were detected in mice. Of note, this approach recapitulated the discovery of a previously known mouse environmentally labile metastable epiallele, CabpIAP. Thus, by querying repetitive DNA in both mouse and humans, we report the first known transposons in humans that respond to perinatal BPA exposure.
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Affiliation(s)
- Christopher Faulk
- a Department of Environmental Health Sciences , University of Michigan , Ann Arbor , MI , USA.,b Department of Animal Science , College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota , Minneapolis , MN , USA
| | - Jung H Kim
- a Department of Environmental Health Sciences , University of Michigan , Ann Arbor , MI , USA
| | - Olivia S Anderson
- c Department of Nutritional Sciences , University of Michigan , Ann Arbor , MI , USA
| | - Muna S Nahar
- a Department of Environmental Health Sciences , University of Michigan , Ann Arbor , MI , USA
| | - Tamara R Jones
- a Department of Environmental Health Sciences , University of Michigan , Ann Arbor , MI , USA
| | - Maureen A Sartor
- d Department of Computational Medicine and Bioinformatics , Medical School, University of Michigan , Ann Arbor , MI , USA
| | - Dana C Dolinoy
- a Department of Environmental Health Sciences , University of Michigan , Ann Arbor , MI , USA.,c Department of Nutritional Sciences , University of Michigan , Ann Arbor , MI , USA
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18
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Bakshi A, Herke SW, Batzer MA, Kim J. DNA methylation variation of human-specific Alu repeats. Epigenetics 2016; 11:163-73. [PMID: 26890526 DOI: 10.1080/15592294.2015.1130518] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have determined the methylation levels associated with 5238 loci belonging to 2 Alu subfamilies, AluYa5 and AluYb8, using high-throughput targeted repeat element bisulfite sequencing (HT-TREBS). The results indicate that ∼90% of loci are repressed by high methylation levels. Of the remaining loci, many of the hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and interindividual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ∼1% of AluYb8 elements in response to tumorigenesis. Simultaneously, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude, even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, approaches such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of interindividual variation in DNA methylation.
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Affiliation(s)
- Arundhati Bakshi
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Scott W Herke
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Mark A Batzer
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Joomyeong Kim
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
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19
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Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT, Batzer MA. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. Genome Biol Evol 2015; 7:2608-22. [PMID: 26319576 PMCID: PMC4607524 DOI: 10.1093/gbe/evv167] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2015] [Indexed: 12/17/2022] Open
Abstract
The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages.
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University
| | | | - Ashley B Hotard
- Department of Biological Sciences, Louisiana State University
| | - Megan C Ranck
- Department of Biological Sciences, Louisiana State University
| | | | - Jessica Storer
- Department of Biological Sciences, Louisiana State University Department of Molecular, Cellular and Developmental Biology, The Ohio State University
| | - Chip Stewart
- Department of Biology, Boston College Cancer Genome Computational Analysis, Cambridge, MA
| | - Gabor T Marth
- Department of Biology, Boston College Eccles Institute of Human Genetics, University of Utah
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University
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20
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Castro-Diaz N, Friedli M, Trono D. Drawing a fine line on endogenous retroelement activity. Mob Genet Elements 2015; 5:1-6. [PMID: 26442176 DOI: 10.1080/2159256x.2015.1006109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 01/05/2023] Open
Abstract
Endogenous retroelements (EREs) are essential motors of evolution yet require careful control to prevent genomic catastrophes, notably during the vulnerable phases of epigenetic reprogramming that occur immediately after fertilization and in germ cells. Accordingly, a variety of mechanisms restrict these mobile genetic units. Previous studies have revealed the importance of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor, KAP1, in the early embryonic silencing of endogenous retroviruses and so-called SVAs, but the implication of this transcriptional repression system in the control of LINE-1, the only known active autonomous retrotransposon in the human genome, was thought to be marginal. Two recent studies straighten the record by revealing that the KRAB/KAP system is key to the control of L1 in embryonic stem (ES) cells, and go further in demonstrating that DNA methylation and KRAB/KAP1-induced repression contribute to this process in an evolutionally dynamic fashion. These results shed light on the delicate equilibrium between higher vertebrates and endogenous retroelements, which are not just genetic invaders calling for strict control but rather a constantly renewed and nicely exploitable source of evolutionary potential.
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Affiliation(s)
- Nathaly Castro-Diaz
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
| | - Marc Friedli
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
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Lee J, Kim YJ, Mun S, Kim HS, Han K. Identification of human-specific AluS elements through comparative genomics. Gene 2014; 555:208-16. [PMID: 25447892 DOI: 10.1016/j.gene.2014.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 01/08/2023]
Abstract
Mobile elements are responsible for ~45% of the human genome. Among them is the Alu element, accounting for 10% of the human genome (>1.1million copies). Several studies of Alu elements have reported that they are frequently involved in human genetic diseases and genomic rearrangements. In this study, we investigated the AluS subfamily, which is a relatively old Alu subfamily and has the highest copy number in primate genomes. Previously, a set of 263 human-specific AluS insertions was identified in the human genome. To validate these, we compared each of the human-specific AluS loci with its pre-insertion site in other primate genomes, including chimpanzee, gorilla, and orangutan. We obtained 24 putative human-specific AluS candidates via the in silico analysis and manual inspection, and then tried to verify them using PCR amplification and DNA sequencing. Through the PCR product sequencing, we were able to detect two instances of near-parallel Alu insertions in nearby sites that led to computational false negatives. Finally, we computationally and experimentally verified 23 human-specific AluS elements. We reported three alternative Alu insertion events, which are accompanied by filler DNA and/or Alu retrotransposition mediated-deletion. Bisulfite sequencing was carried out to examine DNA methylation levels of human-specific AluS elements. The results showed that fixed AluS elements are hypermethylated compared with polymorphic elements, indicating a possible relation between DNA methylation and Alu fixation in the human genome.
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Affiliation(s)
- Jae Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea
| | - Yun-Ji Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.
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22
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Ianc B, Ochis C, Persch R, Popescu O, Damert A. Hominoid composite non-LTR retrotransposons-variety, assembly, evolution, and structural determinants of mobilization. Mol Biol Evol 2014; 31:2847-64. [PMID: 25216663 DOI: 10.1093/molbev/mst256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
SVA (SINE-R-VNTR-Alu) elements constitute the youngest family of composite non-LTR retrotransposons in hominoid primates. The sequence of their assembly, however, remains unclear. Recently, a second family of VNTR-containing composites, LAVA (L1-Alu-VNTR-Alu), has been identified in gibbons. We now report the existence of two additional VNTR composite families, PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu), in the genome of Nomascus leucogenys. Like LAVA, they share the 5'-Alu-like region and VNTR with SVA, but differ at their 3'-ends. The 3'-end of PVA comprises part of the PTGR2 gene, whereas FVA is characterized by the presence of a partial FRAM element in its 3'-domain. Splicing could be identified as the mechanism of acquisition of the variant 3'-ends in all four families of VNTR composites. SVAs have been shown to be mobilized by the L1 protein machinery in trans. A critical role in this process has been ascribed to their 5'-hexameric repeat/ Alu-like region. The Alu-like region displays specific features in each of the VNTR composite families/subfamilies with characteristic deletions found in the evolutionary younger subfamilies. Using reciprocal exchanges between SVA_E and PVA/FVA elements, we demonstrate that the structure, not the presence of the (CCCTCT)n/ Alu-like region determines mobilization capacity. Combination of LAVA and SVA_E domains does not yield any active elements-suggesting the use of different combinations of host factors for the two major groups of VNTR composites. Finally, we demonstrate that the LAVA 3'-L1ME5 fragment attenuates mobilization capacity.
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Affiliation(s)
- Bianca Ianc
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
| | - Cornelia Ochis
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
| | | | - Octavian Popescu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania Institute of Biology, Romanian Academy, Bucharest, Romania
| | - Annette Damert
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
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Dolinoy DC, Faulk C. Introduction: The use of animals models to advance epigenetic science. ILAR J 2014; 53:227-31. [PMID: 23744962 DOI: 10.1093/ilar.53.3-4.227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2200, USA.
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Byun HM, Motta V, Panni T, Bertazzi PA, Apostoli P, Hou L, Baccarelli AA. Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants. Part Fibre Toxicol 2013; 10:28. [PMID: 23855992 PMCID: PMC3717285 DOI: 10.1186/1743-8977-10-28] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 07/05/2013] [Indexed: 02/07/2023] Open
Abstract
Background Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies. Results High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose–response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‒interaction=0.003) and benzene (p‒interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02). Conclusions The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation to airborne pollutants.
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Affiliation(s)
- Hyang-Min Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA.
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Kim YJ, Lee J, Han K. Transposable Elements: No More 'Junk DNA'. Genomics Inform 2012; 10:226-33. [PMID: 23346034 PMCID: PMC3543922 DOI: 10.5808/gi.2012.10.4.226] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/16/2012] [Accepted: 11/17/2012] [Indexed: 01/03/2023] Open
Abstract
Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.
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Affiliation(s)
- Yun-Ji Kim
- Department of Nanobiomedical Science, WCU Research Center, Dankook University, Cheonan 330-714, Korea
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Platt II RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 2012; 500:47-53. [DOI: 10.1016/j.gene.2012.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. Mob DNA 2012; 3:8. [PMID: 22541534 PMCID: PMC3357318 DOI: 10.1186/1759-8753-3-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/30/2012] [Indexed: 01/25/2023] Open
Abstract
Background Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. Results Here we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion. Conclusions This seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.
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Boutin TS, Le Rouzic A, Capy P. How does selfing affect the dynamics of selfish transposable elements? Mob DNA 2012; 3:5. [PMID: 22394388 PMCID: PMC3395816 DOI: 10.1186/1759-8753-3-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/07/2012] [Indexed: 02/02/2023] Open
Abstract
Background Many theoretical models predicting the dynamics of transposable elements (TEs) in genomes, populations, and species have already been proposed. However, most of them only focus on populations of sexual diploid individuals, and TE dynamics in populations partly composed by autogamous individuals remains poorly investigated. To estimate the impact of selfing on TE dynamics, the short- and long-term evolution of TEs was simulated in outcrossing populations with various proportions of selfing individuals. Results Selfing has a deep impact on TE dynamics: the higher the selfing rate, the lower the probability of invasion. Already known non-equilibrium dynamics (complete loss, domestication, cyclical invasion of TEs) can all be described whatever the mating system. However, their pattern and their respective frequencies greatly depend on the selfing rate. For instance, in cyclical dynamics resulting from interactions between autonomous and non-autonomous copies, cycles are faster when the selfing rate increases. Interestingly, an abrupt change in the mating system from sexuality to complete asexuality leads to the loss of all the elements over a few hundred generations. In general, for intermediate selfing rates, the transposition activity remains maintained. Conclusions Our theoretical results evidence that a clear and systematic contrast in TE content according to the mating system is expected, with a smooth transition for intermediate selfing rates. Several parameters impact the TE copy number, and all dynamics described in allogamous populations can be also observed in partly autogamous species. This study thus provides new insights to understand the complex signal from empirical comparison of closely related species with different mating systems.
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Affiliation(s)
- Thibaud S Boutin
- LEGS, CNRS UPR9034, IDEEV FR3284, Avenue de la terrasse, Bat 13, 91198 Gif-sur-Yvette, France.
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Sigurdsson MI, Smith AV, Bjornsson HT, Jonsson JJ. Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome. Gene 2011; 492:104-9. [PMID: 22093876 DOI: 10.1016/j.gene.2011.10.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 10/18/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
Abstract
A potential relationship between transposon-derived repeats (TDR) and human germline methylation is of biological importance since many genes are flanked by TDR and methylation could affect the expression of nearby genes. Furthermore, DNA methylation has been suggested as a global defense mechanism against genome instability threatened by TDR. We studied the correlation between the density of HapMap methyl-associated SNPs (mSNPs), a marker of germline methylation, and proportion of TDR. After correcting for confounding variables, we found a negative correlation between proportion of Alu repeats and mSNP density for 125-1000 kb windows. Similar results were found for the most active subgroup of repeats. In contrast, a negative correlation between proportion of L1 repeats and mSNP density was found only in the larger 1000 kb windows. Using methylation data on germ cells (sperm) from the Human Epigenome Project, we found a lower proportion of Alu repeats adjacent (3-15 kb) to hypermethylated amplicons. On the contrary, there was a higher proportion of L1 repeats in the 3-5 kb of sequence flanking hypermethylated amplicons but not in the 10-15 kb flanks. Our data indicate a differential response to the major repeat families and that DNA methylation is unlikely to be a uniform global defense system against all TDR. It appears to play a role for the L1 subgroup, with sequences adjacent to L1 repeats methylated in response to their proximity. In contrast, sequences adjacent to Alu repeats appear to be hypomethylated, arguing against a role of methylation in germline defense against those elements.
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Affiliation(s)
- Martin I Sigurdsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, IS-101, and Department of Genetics and Molecular Medicine, Landspitali-University Hospital, Reykjavik, IS-101, Iceland
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Cerveau N, Leclercq S, Leroy E, Bouchon D, Cordaux R. Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts. Genome Biol Evol 2011; 3:1175-86. [PMID: 21940637 PMCID: PMC3205602 DOI: 10.1093/gbe/evr096] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Transposable elements (TE) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Long-term TE evolution can readily be reconstructed in eukaryotes, thanks to many degraded copies constituting genomic fossil records of past TE proliferations. By contrast, bacterial genomes usually experience high sequence turnover and short TE retention times, thereby obscuring ancient TE evolutionary patterns. We found that Wolbachia bacterial genomes contain 52–171 insertion sequence (IS) TEs. IS account for 11% of Wolbachia wRi, which is one of the highest IS genomic coverage reported in prokaryotes to date. We show that many IS groups are currently expanding in various Wolbachia genomes and that IS horizontal transfers are frequent among strains, which can explain the apparent synchronicity of these IS proliferations. Remarkably, >70% of Wolbachia IS are nonfunctional. They constitute an unusual bacterial IS genomic fossil record providing direct empirical evidence for a long-term IS evolutionary dynamics following successive periods of intense transpositional activity. Our results show that comprehensive IS annotations have the potential to provide new insights into prokaryote TE evolution and, more generally, prokaryote genome evolution. Indeed, the identification of an important IS genomic fossil record in Wolbachia demonstrates that IS elements are not always of recent origin, contrary to the conventional view of TE evolution in prokaryote genomes. Our results also raise the question whether the abundance of IS fossils is specific to Wolbachia or it may be a general, albeit overlooked, feature of prokaryote genomes.
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Affiliation(s)
- Nicolas Cerveau
- UMR CNRS 6556, Ecologie, Evolution, Symbiose, Université de Poitiers, France
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Mugal CF, Ellegren H. Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol 2011; 12:R58. [PMID: 21696599 PMCID: PMC3218846 DOI: 10.1186/gb-2011-12-6-r58] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 05/04/2011] [Accepted: 06/22/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A major goal in the study of molecular evolution is to unravel the mechanisms that induce variation in the germ line mutation rate and in the genome-wide mutation profile. The rate of germ line mutation is considerably higher for cytosines at CpG sites than for any other nucleotide in the human genome, an increase commonly attributed to cytosine methylation at CpG sites. The CpG mutation rate, however, is not uniform across the genome and, as methylation levels have recently been shown to vary throughout the genome, it has been hypothesized that methylation status may govern variation in the rate of CpG mutation. RESULTS Here, we use genome-wide methylation data from human sperm cells to investigate the impact of DNA methylation on the CpG substitution rate in introns of human genes. We find that there is a significant correlation between the extent of methylation and the substitution rate at CpG sites. Further, we show that the CpG substitution rate is positively correlated with non-CpG divergence, suggesting susceptibility to factors responsible for the general mutation rate in the genome, and negatively correlated with GC content. We only observe a minor contribution of gene expression level, while recombination rate appears to have no significant effect. CONCLUSIONS Our study provides the first direct empirical support for the hypothesis that variation in the level of germ line methylation contributes to substitution rate variation at CpG sites. Moreover, we show that other genomic features also impact on CpG substitution rate variation.
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Affiliation(s)
- Carina F Mugal
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
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Cui F, Sirotin MV, Zhurkin VB. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct 2011; 6:2. [PMID: 21208455 PMCID: PMC3032802 DOI: 10.1186/1745-6150-6-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 01/06/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many p53 in vivo binding sites (BSs) reside in transposable repeats. The relationship between these BSs and functional p53 response elements (REs) remains unknown, however. We sought to understand whether the p53 REs also reside in transposable elements and particularly in the most-abundant Alu repeats. RESULTS We have analyzed ~160 functional p53 REs identified so far and found that 24 of them occur in repeats. More than half of these repeat-associated REs reside in Alu elements. In addition, using a position weight matrix approach, we found ~400,000 potential p53 BSs in Alu elements genome-wide. Importantly, these putative BSs are located in the same regions of Alu repeats as the functional p53 REs - namely, in the vicinity of Boxes A/A' and B of the internal RNA polymerase III promoter. Earlier nucleosome-mapping experiments showed that the Boxes A/A' and B have a different chromatin environment, which is critical for the binding of p53 to DNA. Here, we compare the Alu-residing p53 sites with the corresponding Alu consensus sequences and conclude that the p53 sites likely evolved through two different mechanisms - the sites overlapping with the Boxes A/A' were generated by CG → TG mutations; the other sites apparently pre-existed in the progenitors of several Alu subfamilies, such as AluJo and AluSq. The binding affinity of p53 to the Alu-residing sites generally correlates with the age of Alu subfamilies, so that the strongest sites are embedded in the 'relatively young' Alu repeats. CONCLUSIONS The primate-specific Alu repeats play an important role in shaping the p53 regulatory network in the context of chromatin. One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu transcription, which, in turn, influences expression of the host genes.
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Affiliation(s)
- Feng Cui
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michael V Sirotin
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Kulski JK, Shigenari A, Shiina T, Inoko H. Polymorphic major histocompatibility complex class II Alu insertions at five loci and their association with HLA-DRB1 and -DQB1 in Japanese and Caucasians. ACTA ACUST UNITED AC 2010; 76:35-47. [PMID: 20403137 DOI: 10.1111/j.1399-0039.2010.01465.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated polymorphic Alu insertion (POALIN) frequencies at five loci in the major histocompatibility complex (MHC) class II genomic region to determine their allele and haplotype frequencies and associations with the human leukocyte antigen (HLA)-DRB1 and -DQB1 genes for 100 Japanese, 174 Australian Caucasians and 67 HLA reference cell lines obtained from different ethnic groups. The POALINs varied in frequency between 11% and 57% with significant differences between the Japanese and Caucasians at three loci. One POALIN locus deviated significantly from Hardy-Weinberg equilibrium (HWE) and four POALIN loci were in significant linkage disequilibrium and had a high percentage association with a variety of HLA-DRB1 or -DQB1 two-digit alleles. Inferred haplotype analysis among two-locus, five-locus and seven-locus haplotype structures showed maximum differences between the Japanese and Caucasians with the seven-locus haplotypes. The most common multilocus haplotype in Caucasians was DRB1*1501/DQB1*0602/AluDQ1/AluDRB1/AluORF10/AluDPB2 (6.7%), whereas the second most common allele HLA-DRB1*15 (17.5%) in Japanese was associated with three or four Alu insertions. The HLA class II POALINs also differentiated within and between HLA-DRB1 super-haplotypes DR1, DR8, DR51, DR52 and DR53. This is the first comparative population study of multilocus POALINs in the HLA class II region, which shows that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic markers for the identification of allele and haplotype lineages and variations within the same and/or different populations.
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Affiliation(s)
- J K Kulski
- Centre for Forensic Science, The University of Western Australia, Nedlands, WA, Australia.
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Cordaux R, Sen SK, Konkel MK, Batzer MA. Computational methods for the analysis of primate mobile elements. Methods Mol Biol 2010; 628:137-51. [PMID: 20238080 DOI: 10.1007/978-1-60327-367-1_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including primates. Comparative genome-wide analyses have revealed the considerable structural and functional impact of TE families on primate genomes. Insights into these questions have come in part from the development of computational methods that allow detailed and reliable identification, annotation, and evolutionary analyses of the many TE families that populate primate genomes. Here, we present an overview of these computational methods and describe efficient data mining strategies for providing a comprehensive picture of TE biology in newly available genome sequences.
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Affiliation(s)
- Richard Cordaux
- Laboratoire Ecologie, Evolution et Symbiose, CNRS UMR 6556, Universitè de Poitiers, Poitiers, France
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Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009; 10:691-703. [PMID: 19763152 DOI: 10.1038/nrg2640] [Citation(s) in RCA: 1127] [Impact Index Per Article: 75.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons--including LINE-1, Alu and SVA elements--have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage.
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Affiliation(s)
- Richard Cordaux
- CNRS UMR 6556 Ecologie, Evolution, Symbiose, Université de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France
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Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, Sasaki C, Costa J, Lizardi PM. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene 2009; 448:151-67. [PMID: 19699787 DOI: 10.1016/j.gene.2009.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/19/2009] [Accepted: 08/06/2009] [Indexed: 12/18/2022]
Abstract
Close to 50% of the human genome harbors repetitive sequences originally derived from mobile DNA elements, and in normal cells, this sequence compartment is tightly regulated by epigenetic silencing mechanisms involving chromatin-mediated repression. In cancer cells, repetitive DNA elements suffer abnormal demethylation, with potential loss of silencing. We used a genome-wide microarray approach to measure DNA methylation changes in cancers of the head and neck and to compare these changes to alterations found in adjacent non-tumor tissues. We observed specific alterations at thousands of small clusters of CpG dinucleotides associated with DNA repeats. Among the 257,599 repetitive elements probed, 5% to 8% showed disease-related DNA methylation alterations. In dysplasia, a large number of local events of loss of methylation appear in apparently stochastic fashion. Loss of DNA methylation is most pronounced for certain members of the SVA, HERV, LINE-1P, AluY, and MaLR families. The methylation levels of retrotransposons are discretely stratified, with younger elements being highly methylated in healthy tissues, while in tumors, these young elements suffer the most dramatic loss of methylation. Wilcoxon test statistics reveals that a subset of primate LINE-1 elements is demethylated preferentially in tumors, as compared to non-tumoral adjacent tissue. Sequence analysis of these strongly demethylated elements reveals genomic loci harboring full length, as opposed to truncated elements, while possible enrichment for functional LINE-1 ORFs is weaker. Our analysis suggests that, in non-tumor adjacent tissues, there is generalized and highly variable disruption of epigenetic control across the repetitive DNA compartment, while in tumor cells, a specific subset of LINE-1 retrotransposons that arose during primate evolution suffers the most dramatic DNA methylation alterations.
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Affiliation(s)
- Sebastian Szpakowski
- Interdepartmental Program in Computational, Biology and Bioinformatics, Yale University School of Medicine, Room LH-208, 310 Cedar Street, New Haven, CT 06520, USA
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Kurosaki T, Matsuura T, Ohno K, Ueda S. Alu-mediated acquisition of unstable ATTCT pentanucleotide repeats in the human ATXN10 gene. Mol Biol Evol 2009; 26:2573-9. [PMID: 19651850 DOI: 10.1093/molbev/msp172] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into ATXN10 intron 9; Alu was then inserted in the middle of LINE-1; and endogenous retrovilcus K was lastly retrotransposed in the middle of Alu. The ATTCT repeat was located on the boundary between the 3'-end of the Alu element and the direct repeat arising from LINE-1. We determined nucleotide sequences of the orthologous region of 50 individuals representing 33 primate species and compared them with the human sequence. The analysis revealed that the ATTCT repeat is present only in human and apes. Old World monkeys also possess pentanucleotide repeats, but their motifs are TGTCT and GGTCT. New World monkeys and prosimians are not informative because they lack the corresponding region in ATXN10 intron 9. Our studies dictate two parsimonious scenarios of evolution. First, a TTTCT motif arose from a TTTTT motif at the junction of Alu and LINE-1, which was followed by introduction of A to make an ATTCT motif in hominoids. Second, an ATTCT motif was directly generated from an ancestral ATTTT motif in the common ancestor of catarrhines. We also demonstrate that orangutan uniquely introduced G to make a GTTCT motif and later C to make a GTTCC motif, where newly introduced nucleotides are underlined. Our studies reveal that nucleotide substitutions in a poly(A) tail of the Alu element and the following amplification of pentanucleotides occurred in the lineages of Old World monkeys and hominoids and that unstable ATTCT pentanucleotide repeats originated in the common ancestor of hominoids. These findings also highlight a new aspect of the role of retrotransposons in human disease and evolution, which might be useful in investigating the mystery of human uniqueness.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet 2009; 5:e1000538. [PMID: 19557196 PMCID: PMC2695003 DOI: 10.1371/journal.pgen.1000538] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 05/26/2009] [Indexed: 01/30/2023] Open
Abstract
Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
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Xie H, Wang M, Bonaldo MDF, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 2009; 37:4331-40. [PMID: 19458156 PMCID: PMC2715246 DOI: 10.1093/nar/gkp393] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
DNA methylation, the only known covalent modification of mammalian DNA, occurs primarily in CpG dinucleotides. 51% of CpGs in the human genome reside within repeats, and 25% within Alu elements. Despite that, no method has been reported for large-scale ascertainment of CpG methylation in repeats. Here we describe a sequencing-based strategy for parallel determination of the CpG-methylation status of thousands of Alu repeats, and a computation algorithm to design primers that enable their specific amplification from bisulfite converted genomic DNA. Using a single primer pair, we generated amplicons of high sequence complexity, and derived CpG-methylation data from 31 178 Alu elements and their 5′ flanking sequences, altogether representing over 4 Mb of a human cerebellum epigenome. The analysis of the Alu methylome revealed that the methylation level of Alu elements is high in the intronic and intergenic regions, but low in the regions close to transcription start sites. Several hypomethylated Alu elements were identified and their hypomethylated status verified by pyrosequencing. Interestingly, some Alu elements exhibited a strikingly tissue-specific pattern of methylation. We anticipate the amplicons herein described to prove invaluable as epigenome representations, to monitor epigenomic alterations during normal development, in aging and in diseases such as cancer.
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Affiliation(s)
- Hehuang Xie
- Department of Pediatrics, Division of Anatomic Pathology, Falk Brain Tumor Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60614-3394, USA.
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Styles P, Brookfield JFY. Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons. BMC Evol Biol 2009; 9:102. [PMID: 19442302 PMCID: PMC2686708 DOI: 10.1186/1471-2148-9-102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 05/14/2009] [Indexed: 11/20/2022] Open
Abstract
Background Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. In this study, subfamilies falling on the AluYi and AluYh lineages, and the AluYg6 subfamily, are assessed for the presence of secondary source genes, and the influence of gene conversion on the AluYh and AluYi lineages is also described. Results The AluYh7 and AluYi6 subfamilies appear to contain multiple source genes. The novel subfamilies AluYh3a1 and AluYh3a3 are described, for which there is no convincing evidence to suggest the presence of secondary sources. The mutational substructure of AluYh3a3 can be explained completely by inference of single master gene. A complete backwards gene conversion event appears to have inactivated the AluYh3a3 master gene in humans. Polymorphism data suggest a larger number of secondary source elements may be active in the AluYg6 family than previously thought. Conclusion It is clear that there is considerable variation in the number of source genes present in each of the young Alu subfamilies. This can range from a single master source gene, as for AluYh3a3, to as many as 14 source elements in AluYi6.
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Affiliation(s)
- Pamela Styles
- Institute of Genetics, School of Biology, University of Nottingham, Nottingham, UK.
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Marchani EE, Xing J, Witherspoon DJ, Jorde LB, Rogers AR. Estimating the age of retrotransposon subfamilies using maximum likelihood. Genomics 2009; 94:78-82. [PMID: 19379804 DOI: 10.1016/j.ygeno.2009.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 04/10/2009] [Accepted: 04/11/2009] [Indexed: 11/29/2022]
Abstract
We present a maximum likelihood model to estimate the age of retrotransposon subfamilies. This method is designed around a master gene model which assumes a constant retrotransposition rate. The statistical properties of this model and an ad hoc estimation procedure are compared using two simulated data sets. We also test whether each estimation procedure is robust to violation of the master gene model. According to our results, both estimation procedures are accurate under the master gene model. While both methods tend to overestimate ages under the intermediate model, the maximum likelihood estimate is significantly less inflated than the ad hoc estimate. We estimate the ages of two subfamilies of human-specific LINE-I insertions using both estimation procedures. By calculating confidence intervals around the maximum likelihood estimate, our model can both provide an estimate of retrotransposon subfamily age and describe the range of subfamily ages consistent with the data.
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Affiliation(s)
- Elizabeth E Marchani
- Division of Medical Genetics, University of Washington, BOX 357720, Seattle, WA 98195, USA.
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Park ES, Huh JW, Kim TH, Kwak KD, Kim W, Kim HS. Analysis of newly identified low copy AluYj subfamily. Genes Genet Syst 2009; 80:415-22. [PMID: 16501310 DOI: 10.1266/ggs.80.415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human specific AluY elements were investigated by comparative analysis between human chromosome 21 and chimpanzee chromosome 22. Human specific AluY element was identified on human chromosome 21q22 (accession no. AL163282), and then that was a new member of AluYj subfamily. From the bioinformatic analysis, AluYj subfamily was investigated in human whole genome using AluYj4 consensus sequence (accession no. AL163282). Thirteen members of the AluYj4 elements (4 diagnostic mutations) and eight members of the AluYj3 elements (3 diagnostic mutations) were identified with distinct diagnostic mutation from AluY consensus sequence. The results of the molecular clock calculation of non-CpG region substitution indicated that, AluYj4 elements (2.1 million years old) may be proliferated more recent time than AluYj3 elements (14.1 million years old). For the verification of recent insertion time, four of AluYj4 elements (ch2-AC017101, ch10-AC044786, ch12-AC007656 and ch21-AL163282) from human chromosomes 2, 10, 12, 21 were analyzed by PCR amplification using various human and primate DNA samples. Though, no polymorphism was detected in human population, we identified the new AluYj4 subfamily as the human specific elements.
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Affiliation(s)
- Eun-Sil Park
- Division of Biological Sciences, College of Natural Sciences, Pusan National University, Buscan, Korea
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Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M. Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet 2008; 25:63-6. [PMID: 19101055 DOI: 10.1016/j.tig.2008.11.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 11/19/2008] [Accepted: 11/20/2008] [Indexed: 11/28/2022]
Abstract
The formation of transcription-factor-binding sites is an important evolutionary process. Here, we show that methylation and deamination of CpG dinucleotides generate in vivo p53-binding sites in numerous Alu elements and in non-repetitive DNA in a species-specific manner. In light of this, we propose that the deamination of methylated CpGs constitutes a universal mechanism for de novo generation of various transcription-factor-binding sites in Alus.
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Affiliation(s)
- Tomasz Zemojtel
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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Chen C, Ara T, Gautheret D. Using Alu elements as polyadenylation sites: A case of retroposon exaptation. Mol Biol Evol 2008; 26:327-34. [PMID: 18984903 DOI: 10.1093/molbev/msn249] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Of the 1.1 million Alu retroposons in the human genome, about 10,000 are inserted in the 3' untranslated regions (UTR) of protein-coding genes and 1% of these (107 events) are active as polyadenylation sites (PASs). Strikingly, although Alu's in 3' UTR are indifferently inserted in the forward or reverse direction, 99% of polyadenylation-active Alu sequences are forward oriented. Consensus Alu+ sequences contain sites that can give rise to polyadenylation signals and enhancers through a few point mutations. We found that the strand bias of polyadenylation-active Alu's reflects a radical difference in the fitness of sense and antisense Alu's toward cleavage/polyadenylation activity. In contrast to previous beliefs, Alu inserts do not necessarily represent weak or cryptic PASs; instead, they often constitute the major or the unique PAS in a gene, adding to the growing list of Alu exaptations. Finally, some Alu-borne PASs are intronic and produce truncated transcripts that may impact gene function and/or contribute to gene remodeling.
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Affiliation(s)
- Chongjian Chen
- Institut de Génétique et Microbiologie, Université Paris, Orsay, France
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46
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Tomilin NV. Regulation of mammalian gene expression by retroelements and non-coding tandem repeats. Bioessays 2008; 30:338-48. [PMID: 18348251 DOI: 10.1002/bies.20741] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Genomes of higher eukaryotes contain abundant non-coding repeated sequences whose overall biological impact is unclear. They comprise two categories. The first consists of retrotransposon-derived elements. These are three major families of retroelements (LINEs, SINEs and LTRs). SINEs are clustered in gene-rich regions and are found in promoters of genes while LINEs are concentrated in gene-poor regions and are depleted from promoters. The second class consists of non-coding tandem repeats (satellite DNAs and TTAGGG arrays), which are associated with mammalian centromeres, heterochromatin and telomeres. Terminal TTAGGG arrays are involved in telomere capping and satellite DNAs are located in heterochromatin, which is implicated in transcription silencing by gene repositioning (relocalization). It is unknown whether interstitial TTAGGG sequences, which are present in many vertebrates, have a function. Here, evidence will be presented that retroelements and TTAGGG arrays are involved in regulation of gene expression. Retroelements can provide binding sites for transcription factors and protect promoter CpG islands from repressive chromatin modifications, and may be also involved in nuclear compartmentalization of transcriptionally active and inactive domains. Interstitial telomere-like sequences can form dynamically maintained three-dimensional nuclear networks of transcriptionally inactive domains, which may be involved in transcription silencing like classic heterochromatin.
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Affiliation(s)
- Nikolai V Tomilin
- Institute of Cytology, Russian Academy of Sciences, 194064 St.Petersburg, Tikchoretskii Av. 4, Russia.
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Harony H, Ankri S. What do unicellular organisms teach us about DNA methylation? Trends Parasitol 2008; 24:205-9. [PMID: 18403268 DOI: 10.1016/j.pt.2008.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 02/01/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
Abstract
DNA methylation is an epigenetic hallmark that has been studied intensively in mammals and plants. However, knowledge of this phenomenon in unicellular organisms is scanty. Examining epigenetic regulation, and more specifically DNA methylation, in these organisms represents a unique opportunity to better understand their biology. The determination of their methylation status is often complicated by the presence of several differentiation stages in their life cycle. This article focuses on some recent advances that have revealed the unexpected nature of the epigenetic determinants present in protozoa. The role of the enigmatic DNA methyltransferase Dnmt2 in unicellular organisms is discussed.
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Affiliation(s)
- Hala Harony
- Department of Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, the Rappaport Institute, 31096 Haifa, Israel
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Ray DA, Feschotte C, Pagan HJT, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res 2008; 18:717-28. [PMID: 18340040 DOI: 10.1101/gr.071886.107] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and Helitron elements, two distinct groups of DNA transposons, in the lineage of the vespertilionid bat Myotis lucifugus. Here, we describe seven additional families that have also been recently active in the bat lineage. Early vespertilionid genome evolution was dominated by the activity of Helitrons, mariner-like and Tc2-like elements. This was followed by the colonization of Tc1-like elements, and by a more recent explosion of hAT-like elements. Finally, and most recently, piggyBac-like elements have amplified within the Myotis genome and our results indicate that one of these families is probably still expanding in natural populations. Together, these data suggest that there has been tremendous recent activity of various DNA transposons in the bat lineage that far exceeds those previously reported for any mammalian lineage. The diverse and recent populations of DNA transposons in genus Myotis will provide an unprecedented opportunity to study the impact of this class of elements on mammalian genome evolution and to better understand what makes some species more susceptible to invasion by genomic parasites than others.
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Affiliation(s)
- David A Ray
- Department of Biology, West Virginia University, Morgantown, West Virginia 26506, USA.
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Rodriguez J, Vives L, Jordà M, Morales C, Muñoz M, Vendrell E, Peinado MA. Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. Nucleic Acids Res 2007; 36:770-84. [PMID: 18084025 PMCID: PMC2241897 DOI: 10.1093/nar/gkm1105] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Methylation of the cytosine is the most frequent epigenetic modification of DNA in mammalian cells. In humans, most of the methylated cytosines are found in CpG-rich sequences within tandem and interspersed repeats that make up to 45% of the human genome, being Alu repeats the most common family. Demethylation of Alu elements occurs in aging and cancer processes and has been associated with gene reactivation and genomic instability. By targeting the unmethylated SmaI site within the Alu sequence as a surrogate marker, we have quantified and identified unmethylated Alu elements on the genomic scale. Normal colon epithelial cells contain in average 25 486 ± 10 157 unmethylated Alu's per haploid genome, while in tumor cells this figure is 41 995 ± 17 187 (P = 0.004). There is an inverse relationship in Alu families with respect to their age and methylation status: the youngest elements exhibit the highest prevalence of the SmaI site (AluY: 42%; AluS: 18%, AluJ: 5%) but the lower rates of unmethylation (AluY: 1.65%; AluS: 3.1%, AluJ: 12%). Data are consistent with a stronger silencing pressure on the youngest repetitive elements, which are closer to genes. Further insights into the functional implications of atypical unmethylation states in Alu elements will surely contribute to decipher genomic organization and gene regulation in complex organisms.
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Affiliation(s)
- Jairo Rodriguez
- Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet, Catalonia, Spain
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50
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Kim HH, Park JH, Jeong KS, Lee S. Determining the global DNA methylation status of rat according to the identifier repetitive elements. Electrophoresis 2007; 28:3854-61. [DOI: 10.1002/elps.200600733] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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