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López JO, Quiñones JL, Martínez ED. Improved LINE-1 Detection through Pattern Matching by Increasing Probe Length. BIOLOGY 2024; 13:236. [PMID: 38666848 PMCID: PMC11047891 DOI: 10.3390/biology13040236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created to detect L1s by using a fixed pre-determined set of 50-mer probes and a pattern-matching algorithm. L1PD uses a novel seed-and-pattern-match strategy as opposed to the well-known seed-and-extend strategy employed by other tools. This study discusses an improved version of L1PD that shows how increasing the size of the k-mer probes from 50 to 75 or to 100 yields better results, as evidenced by experiments showing higher precision and recall when compared to the 50-mers. The probe-generation process was updated and the corresponding software is now shared so that users may generate probes for other reference genomes (with certain limitations). Additionally, L1PD was applied to other non-human genomes, such as dogs, horses, and cows, to further validate the pattern-matching strategy. The improved version of L1PD proves to be an efficient and promising approach for L1 detection.
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Affiliation(s)
- Juan O. López
- Department of Computer Science, University of Puerto Rico at Arecibo, Arecibo 00612, Puerto Rico; (J.L.Q.); (E.D.M.)
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2
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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3
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Walter NG. Are non-protein coding RNAs junk or treasure?: An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non-functional or functional RNAs. Bioessays 2024; 46:e2300201. [PMID: 38351661 DOI: 10.1002/bies.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 03/28/2024]
Abstract
The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non-protein coding, or non-coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is "junk", a term still championed by some geneticists and evolutionary biologists. In contrast, molecular biologists and biochemists studying the vast number of transcripts produced from most of this genome "junk" often surmise that these ncRNAs have biological significance. What gives? This essay contrasts the two opposing, extant viewpoints, aiming to explain their bases, which arise from distinct reference frames of the underlying scientific disciplines. Finally, it aims to reconcile these divergent mindsets in hopes of stimulating synergy between scientific fields.
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Affiliation(s)
- Nils G Walter
- Center for RNA Biomedicine, Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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4
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [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] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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5
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Bilgrav Saether K, Nilsson D, Thonberg H, Tham E, Ameur A, Eisfeldt J, Lindstrand A. Transposable element insertions in 1000 Swedish individuals. PLoS One 2023; 18:e0289346. [PMID: 37506127 PMCID: PMC10381067 DOI: 10.1371/journal.pone.0289346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
The majority of rare diseases are genetic, and regardless of advanced high-throughput genomics-based investigations, 60% of patients remain undiagnosed. A major factor limiting our ability to identify disease-causing alterations is a poor understanding of the morbid and normal human genome. A major genomic contributor of which function and distribution remain largely unstudied are the transposable elements (TE), which constitute 50% of our genome. Here we aim to resolve this knowledge gap and increase the diagnostic yield of rare disease patients investigated with clinical genome sequencing. To this end we characterized TE insertions in 1000 Swedish individuals from the SweGen dataset and 2504 individuals from the 1000 Genomes Project (1KGP), creating seven population-specific TE insertion databases. Of note, 66% of TE insertions in SweGen were present at >1% in the 1KGP databases, proving that most insertions are common across populations. Focusing on the rare TE insertions, we show that even though ~0.7% of those insertions affect protein coding genes, they rarely affect known disease casing genes (<0.1%). Finally, we applied a TE insertion identification workflow on two clinical cases where disease causing TE insertions were suspected and could verify the presence of pathogenic TE insertions in both. Altogether we demonstrate the importance of TE insertion detection and highlight possible clinical implications in rare disease diagnostics.
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Affiliation(s)
- Kristine Bilgrav Saether
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Oláh E. Learning from cancer to address COVID-19. Biol Futur 2023:10.1007/s42977-023-00156-5. [PMID: 37410273 DOI: 10.1007/s42977-023-00156-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/24/2023] [Indexed: 07/07/2023]
Abstract
Patients with cancer have been disproportionately affected by the novel coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Knowledge collected during the last three decades of cancer research has helped the medical research community worldwide to respond to many of the challenges raised by COVID-19, during the pandemic. The review, briefly summarizes the underlying biology and risk factors of COVID-19 and cancer, and aims to present recent evidence on cellular and molecular relationship between the two diseases, with a focus on those that are related to the hallmarks of cancer and uncovered in the first less than three years of the pandemic (2020-2022). This may not only help answer the question "Why cancer patients are considered to be at a particularly high risk of developing severe COVID-19 illness?", but also helped treatments of patients during the COVID-19 pandemic. The last session highlights the pioneering mRNA studies and the breakthrough discovery on nucleoside-modifications of mRNA by Katalin Karikó, which led to the innovation and development of the mRNA-based SARSCoV-2 vaccines saving lives of millions and also opened the door for a new era of vaccines and a new class of therapeutics.
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Affiliation(s)
- Edit Oláh
- Department of Molecular Genetics, National Institute of Oncology, Ráth György u. 7-9, Budapest, 1122, Hungary.
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7
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Berteli TS, Wang F, Navarro PA, Kohlrausch FB, Keefe DL. A pilot study of LINE-1 copy number and telomere length with aging in human sperm. J Assist Reprod Genet 2023:10.1007/s10815-023-02857-1. [PMID: 37382785 PMCID: PMC10371944 DOI: 10.1007/s10815-023-02857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/30/2023] Open
Abstract
PURPOSE Unlike other cells in the body, in sperm, telomere length (TL) increases with age. TL can regulate nearby genes, and the subtelomeric region is rich in retrotransposons. We hypothesized that age-related telomere lengthening in sperm might suppress Long Interspersed Element 1 (LINE-1/L1), the only competent retrotransposon in humans. METHODS We measured L1 copy number (L1-CN) and sperm telomere length (STL) from young and older men to evaluate the relationship between age, TL and L1-CN. We also evaluated L1-CN and TL in individual sperm to determine whether these variables influence sperm morphology. STL was assayed by Multiplex quantitative polymerase chain reaction method (mmqPCR) and L1-CN by Quantitative polymerase chain reaction (qPCR). RESULTS We found that STL increased, and L1-CN decreased significantly with paternal age. STL in normal single sperm was significantly higher than in abnormal sperm. L1-CN did not differ between normal and abnormal sperm. Furthermore, morphologically normal sperm have longer telomeres than abnormal sperm. CONCLUSIONS Elongation of telomeres in the male germline could repress retrotransposition, which tends to increase with cellular aging. More studies in larger cohorts across a wide age span are needed to confirm our conclusions and explore their biological and clinical significance.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
- Human Genetics Laboratory, Fluminense Federal University, Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
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Yang R, Yang Y, Yang L, Chen H, Zhong W, Zhu L. First insight into the sex-dependent accumulation, tissue distribution and potential toxicities of 2-ethylhexyl diphenyl phosphate and its metabolites in adult zebrafish. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131299. [PMID: 37027911 DOI: 10.1016/j.jhazmat.2023.131299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/05/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
The 2-ethylhexyl diphenyl phosphate (EHDPHP), a primary organophosphorus flame retardant used in various industrial products, is prone to biotransformation. However, there is a knowledge gap on the sex- and tissue-specific accumulation and potential toxicities of EHDPHP (M1) and its metabolites (M2-M16). In this study, adult zebrafish (Danio rerio) were exposed to EHDPHP (0, 5, 35 and 245 µg/L) for 21-day, which was followed by 7-day depuration. The bioconcentration factor (BCF) of EHDPHP in female zebrafish was 26.2 ± 7.7% lower than in males due to the lower uptake rate (ku) while higher depuration rate (kd) in the females. The regular ovulation and higher metabolic efficiency promoted elimination from female zebrafish, thus leading to much less (28-44%) accumulation of ∑(M1-M16) in female zebrafish. They exhibited the highest accumulation in the liver and intestine in both sexes, which might be regulated by tissue-specific transporters and histones evidenced by molecular docking results. Intestine microbiota analysis further revealed that female zebrafish were more susceptible to EHDPHP exposure, with more significant changes in phenotype number and KEGG pathways in female than male fish. Disease prediction results suggested that EHDPHP exposure might cause cancers, cardiovascular diseases as well as endocrine disorders in both sexes. These results provide a comprehensive understanding of the sex-dependent accumulation and toxicity of EHDPHP and its metabolites.
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Affiliation(s)
- Rongyan Yang
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Yi Yang
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Liping Yang
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Hao Chen
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
| | - Wenjue Zhong
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China.
| | - Lingyan Zhu
- Key Laboratory of Pollution Processes and Environmental Criteria of Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering of Nankai University, Tianjin 300350, China
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9
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Mosaddeghi P, Farahmandnejad M, Zarshenas MM. The role of transposable elements in aging and cancer. Biogerontology 2023:10.1007/s10522-023-10028-z. [PMID: 37017895 DOI: 10.1007/s10522-023-10028-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023]
Abstract
Transposable elements (TEs) constitute a large portion of the human genome. Various mechanisms at the transcription and post-transcription levels developed to suppress TE activity in healthy conditions. However, a growing body of evidence suggests that TE dysregulation is involved in various human diseases, including age-related diseases and cancer. In this review, we explained how sensing TEs by the immune system could induce innate immune responses, chronic inflammation, and following age-related diseases. We also noted that inflammageing and exogenous carcinogens could trigger the upregulation of TEs in precancerous cells. Increased inflammation could enhance epigenetic plasticity and upregulation of early developmental TEs, which rewires the transcriptional networks and gift the survival advantage to the precancerous cells. In addition, upregulated TEs could induce genome instability, activation of oncogenes, or inhibition of tumor suppressors and consequent cancer initiation and progression. So, we suggest that TEs could be considered therapeutic targets in aging and cancer.
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Affiliation(s)
- Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mitra Farahmandnejad
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad M Zarshenas
- Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Cao J, Yu T, Xu B, Hu Z, Zhang XO, Theurkauf W, Weng Z. Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic Acids Res 2023; 51:2066-2086. [PMID: 36762470 PMCID: PMC10018349 DOI: 10.1093/nar/gkad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Transposons are mobile genetic elements prevalent in the genomes of most species. The distribution of transposons within a genome reflects the actions of two opposing processes: initial insertion site selection, and selective pressure from the host. By analyzing whole-genome sequencing data from transposon-activated Drosophila melanogaster, we identified 43 316 de novo and 237 germline insertions from four long-terminal-repeat (LTR) transposons, one LINE transposon (I-element), and one DNA transposon (P-element). We found that all transposon types favored insertion into promoters de novo, but otherwise displayed distinct insertion patterns. De novo and germline P-element insertions preferred replication origins, often landing in a narrow region around transcription start sites and in regions of high chromatin accessibility. De novo LTR transposon insertions preferred regions with high H3K36me3, promoters and exons of active genes; within genes, LTR insertion frequency correlated with gene expression. De novo I-element insertion density increased with distance from the centromere. Germline I-element and LTR transposon insertions were depleted in promoters and exons, suggesting strong selective pressure to remove transposons from functional elements. Transposon movement is associated with genome evolution and disease; therefore, our results can improve our understanding of genome and disease biology.
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Affiliation(s)
| | - Tianxiong Yu
- Correspondence may also be addressed to Tianxiong Yu. Tel: +1 774 641 0409; Fax: +1 508 856 0017;
| | - Bo Xu
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongren Hu
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-ou Zhang
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- To whom correspondence should be addressed. Tel: +1 508 856 8866; Fax: +1 508 856 0017;
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Magrinelli F, Rocca C, Simone R, Zenezini Chiozzi R, Jaunmuktane Z, Mencacci NE, Tinazzi M, Jayawant S, Nemeth AH, Demidov G, Houlden H, Bhatia KP. Detection and Characterization of a De Novo Alu Retrotransposition Event Causing NKX2-1-Related Disorder. Mov Disord 2023; 38:347-353. [PMID: 36420574 DOI: 10.1002/mds.29280] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/17/2022] [Accepted: 11/06/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Heterozygous NKX2-1 loss-of-function variants cause combinations of hyperkinetic movement disorders (MDs, particularly childhood-onset chorea), pulmonary dysfunction, and hypothyroidism. Mobile element insertions (MEIs) are potential disease-causing structural variants whose detection in routine diagnostics remains challenging. OBJECTIVE To establish the molecular diagnosis of two first-degree relatives with clinically suspected NKX2-1-related disorder who had negative NKX2-1 Sanger (SS), whole-exome (WES), and whole-genome (WGS) sequencing. METHODS The proband's WES was analyzed for MEIs. A candidate MEI in NKX2-1 underwent optimized SS after plasmid cloning. Functional studies exploring NKX2-1 haploinsufficiency at RNA and protein levels were performed. RESULTS A 347-bp AluYa5 insertion with a 65-bp poly-A tail followed by a 16-bp duplication of the pre-insertion wild-type sequence in exon 3 of NKX2-1 (ENST00000354822.7:c.556_557insAlu541_556dup) segregated with the disease phenotype. CONCLUSIONS We identified a de novo exonic AluYa5 insertion causing NKX2-1-related disorder in SS/WES/WGS-negative cases, suggesting that MEI analysis of short-read sequencing data or targeted long-read sequencing could unmask the molecular diagnosis of unsolved MD cases. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
- William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Roberto Simone
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | | | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Niccolò E Mencacci
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michele Tinazzi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Sandeep Jayawant
- Paediatric Neurology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
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12
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The Power of Clinical Diagnosis for Deciphering Complex Genetic Mechanisms in Rare Diseases. Genes (Basel) 2023; 14:genes14010196. [PMID: 36672937 PMCID: PMC9858967 DOI: 10.3390/genes14010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Complex genetic disease mechanisms, such as structural or non-coding variants, currently pose a substantial difficulty in frontline diagnostic tests. They thus may account for most unsolved rare disease patients regardless of the clinical phenotype. However, the clinical diagnosis can narrow the genetic focus to just a couple of genes for patients with well-established syndromes defined by prominent physical and/or unique biochemical phenotypes, allowing deeper analyses to consider complex genetic origin. Then, clinical-diagnosis-driven genome sequencing strategies may expedite the development of testing and analytical methods to account for complex disease mechanisms as well as to advance functional assays for the confirmation of complex variants, clinical management, and the development of new therapies.
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13
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A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. GeroScience 2022; 44:1525-1550. [PMID: 35585302 PMCID: PMC9213607 DOI: 10.1007/s11357-022-00580-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
Recent reports have suggested that the reactivation of otherwise transcriptionally silent transposable elements (TEs) might induce brain degeneration, either by dysregulating the expression of genes and pathways implicated in cognitive decline and dementia or through the induction of immune-mediated neuroinflammation resulting in the elimination of neural and glial cells. In the work we present here, we test the hypothesis that differentially expressed TEs in blood could be used as biomarkers of cognitive decline and development of AD. To this aim, we used a sample of aging subjects (age > 70) that developed late-onset Alzheimer’s disease (LOAD) over a relatively short period of time (12–48 months), for which blood was available before and after their phenoconversion, and a group of cognitive stable subjects as controls. We applied our developed and validated customized pipeline that allows the identification, characterization, and quantification of the differentially expressed (DE) TEs before and after the onset of manifest LOAD, through analyses of RNA-Seq data. We compared the level of DE TEs within more than 600,000 TE-mapping RNA transcripts from 25 individuals, whose specimens we obtained before and after their phenotypic conversion (phenoconversion) to LOAD, and discovered that 1790 TE transcripts showed significant expression differences between these two timepoints (logFC ± 1.5, logCMP > 5.3, nominal p value < 0.01). These DE transcripts mapped both over- and under-expressed TE elements. Occurring before the clinical phenoconversion, this TE storm features significant increases in DE transcripts of LINEs, LTRs, and SVAs, while those for SINEs are significantly depleted. These dysregulations end with signs of manifest LOAD. This set of highly DE transcripts generates a TE transcriptional profile that accurately discriminates the before and after phenoconversion states of these subjects. Our findings suggest that a storm of DE TEs occurs before phenoconversion from normal cognition to manifest LOAD in risk individuals compared to controls, and may provide useful blood-based biomarkers for heralding such a clinical transition, also suggesting that TEs can indeed participate in the complex process of neurodegeneration.
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14
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Varela RB, Cararo JH, Tye SJ, Carvalho AF, Valvassori SS, Fries GR, Quevedo J. Contributions of epigenetic inheritance to the predisposition of major psychiatric disorders: theoretical framework, evidence, and implications. Neurosci Biobehav Rev 2022; 135:104579. [DOI: 10.1016/j.neubiorev.2022.104579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
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15
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DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies. Genes (Basel) 2021; 13:genes13010009. [PMID: 35052350 PMCID: PMC8775202 DOI: 10.3390/genes13010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/08/2023] Open
Abstract
Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) are designed for subsequent genome repeat masking, often leaving aside the element lineage classification and its protein domain composition. Additionally, studies focused on the diversity and evolution of a particular group of retrotransposons often require substantial customization efforts from researchers to adapt existing software to their needs. Here, we developed a computational pipeline to mine sequences of protein-coding retrotransposons based on the sequences of their conserved protein domains—DARTS (Domain-Associated Retrotransposon Search). Using the most abundant group of TEs in plants—long terminal repeat (LTR) retrotransposons (LTR-RTs)—we show that DARTS has radically higher sensitivity for LTR-RT identification compared to the widely accepted tool LTRharvest. DARTS can be easily customized for specific user needs. As a result, DARTS returns a set of structurally annotated nucleotide and amino acid sequences which can be readily used in subsequent comparative and phylogenetic analyses. DARTS may facilitate researchers interested in the discovery and detailed analysis of the diversity and evolution of retrotransposons, LTR-RTs, and other protein-coding TEs.
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16
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Rotondo JC, Lanzillotti C, Mazziotta C, Tognon M, Martini F. Epigenetics of Male Infertility: The Role of DNA Methylation. Front Cell Dev Biol 2021; 9:689624. [PMID: 34368137 PMCID: PMC8339558 DOI: 10.3389/fcell.2021.689624] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/17/2021] [Indexed: 12/18/2022] Open
Abstract
In recent years, a number of studies focused on the role of epigenetics, including DNA methylation, in spermatogenesis and male infertility. We aimed to provide an overview of the knowledge concerning the gene and genome methylation and its regulation during spermatogenesis, specifically in the context of male infertility etiopathogenesis. Overall, the findings support the hypothesis that sperm DNA methylation is associated with sperm alterations and infertility. Several genes have been found to be differentially methylated in relation to impaired spermatogenesis and/or reproductive dysfunction. Particularly, DNA methylation defects of MEST and H19 within imprinted genes and MTHFR within non-imprinted genes have been repeatedly linked with male infertility. A deep knowledge of sperm DNA methylation status in association with reduced reproductive potential could improve the development of novel diagnostic tools for this disease. Further studies are needed to better elucidate the mechanisms affecting methylation in sperm and their impact on male infertility.
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Affiliation(s)
- John Charles Rotondo
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Carmen Lanzillotti
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Mazziotta
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Laboratories of Cell Biology and Molecular Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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17
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Yu T, Huang X, Dou S, Tang X, Luo S, Theurkauf WE, Lu J, Weng Z. A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acids Res 2021; 49:e44. [PMID: 33511407 PMCID: PMC8096211 DOI: 10.1093/nar/gkab010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 02/01/2023] Open
Abstract
Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo ‘singleton’ insertion frequencies in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by de-repressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2.
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Affiliation(s)
- Tianxiong Yu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiao Huang
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shengqian Dou
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shiqi Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Weng
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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18
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Liehr T. Repetitive Elements in Humans. Int J Mol Sci 2021; 22:ijms22042072. [PMID: 33669810 PMCID: PMC7922087 DOI: 10.3390/ijms22042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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19
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Marthey S, Estellé J, Blin A, Wahlberg P, Créchet F, Lecardonnel J, Tessiot F, Rogel-Gaillard C, Bourneuf E. Transcription from a gene desert in a melanoma porcine model. Mol Genet Genomics 2020; 295:1239-1252. [PMID: 32529263 DOI: 10.1007/s00438-020-01694-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/03/2020] [Indexed: 01/11/2023]
Abstract
The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients' care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM model. Indeed, a large region of the Sus scrofa chromosome 1 has been identified by linkage and association analyses, but the causal mechanisms have remained elusive. To deepen the analysis of this candidate region, a dedicated SNP panel was used to fine map the locus, downsizing the interval to less than 2 Mb, in a genomic region located within a large gene desert. Transcription from this locus was addressed using a tiling array strategy and further validated by RT-PCR in a large panel of tissues. Overall, the gene desert showed an extensive transcriptional landscape, notably dominated by repeated element transcription in tumor and fetal tissues. The transcription of LINE-1 and PERVs has been confirmed in skin and tumor samples from MeLiM pigs. In conclusion, although this study still does not identify a candidate mutation for melanoma occurrence or progression, it highlights a potential role of repeated element transcriptional activity in the MeLiM model.
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Affiliation(s)
- S Marthey
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - A Blin
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Muséum national d'histoire naturelle, Centre national de la recherche scientifique, UMS 2700 2AD, CP51, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - P Wahlberg
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - F Créchet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - F Tessiot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - C Rogel-Gaillard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - E Bourneuf
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- LCE, IRCM, DRF, CEA, Université Paris-Saclay, 92260, Fontenay-aux-Roses, France.
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20
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Lee CT, Cavalcante RG, Lee C, Qin T, Patil S, Wang S, Tsai Z, Boyle AP, Sartor MA. Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. NAR Genom Bioinform 2020; 2:lqaa006. [PMID: 32051932 PMCID: PMC7003681 DOI: 10.1093/nargab/lqaa006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/12/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and Broad-Enrich for broad regions. Here, we introduce Poly-Enrich, which has wider applicability, additional capabilities and models the number of peaks assigned to a gene using a generalized additive model with a negative binomial family to determine gene set enrichment, while adjusting for gene locus length. As opposed to ChIP-Enrich, Poly-Enrich works well even when nearly all genes have a peak, illustrated by using Poly-Enrich to characterize pathways and types of genic regions enriched with different families of repetitive elements. By comparing Poly-Enrich and ChIP-Enrich results with ENCODE ChIP-seq data, we found that the optimal test depends more on the pathway being regulated than on properties of the transcription factors. Using known transcription factor functions, we discovered clusters of related biological processes consistently better modeled with Poly-Enrich. This suggests that the regulation of certain processes may be modified by multiple binding events, better modeled by a count-based method. Our new hybrid method automatically uses the optimal method for each gene set, with correct FDR-adjustment.
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Affiliation(s)
- Christopher T Lee
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chee Lee
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Snehal Patil
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuze Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zing T Y Tsai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Biostatistics Department, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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Abstract
Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both
in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
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22
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Batista RL, Yamaguchi K, Rodrigues ADS, Nishi MY, Goodier JL, Carvalho LR, Domenice S, Costa EMF, Kazazian HH, Mendonca BB. Mobile DNA in Endocrinology: LINE-1 Retrotransposon Causing Partial Androgen Insensitivity Syndrome. J Clin Endocrinol Metab 2019; 104:6385-6390. [PMID: 31393562 PMCID: PMC6834070 DOI: 10.1210/jc.2019-00144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/02/2019] [Indexed: 11/19/2022]
Abstract
CONTEXT Androgen insensitivity syndrome (AIS) is the most common cause of disorders of sex development in 46,XY individuals. It is an X-linked condition usually caused by pathogenic allelic variants in the androgen receptor (AR) gene. The phenotype depends on the AR variant, ranging from severe undervirilization (complete AIS) to several degrees of external genitalia undervirilization. Although 90% of those with complete AIS will have AR mutations, this will only be true for 40% of those with partial AIS (PAIS). OBJECTIVE To identify the genetic etiology of AIS in a large multigenerational family with the PAIS phenotype. PARTICIPANTS Nine affected individuals with clinical and laboratory findings consistent with PAIS and a normal exonic AR sequencing. SETTINGS Endocrine clinic and genetic institute from two academic referral centers. DESIGN Analysis of whole exons of the AR gene, including splicing regions, was performed, followed by sequencing of the 5'untranslated region (UTR) of the AR gene. Detailed phenotyping was performed at the initial diagnosis and long-term follow-up, and circulating levels of steroid gonadal hormones were measured in all affected individuals. AR expression was measured using RT-PCR and cultured fibroblasts. RESULTS All 46,XY family members with PAIS had inherited, in hemizygosity, a complex defect (∼1100 bp) in the 5'UTR region of the AR surrounded by a duplicated 18-bp sequence (target site duplication). This sequence is 99.7% similar to an active, long, interspersed element present on the X chromosome (AC002980; Xq22.2), which was inserted in the 5'UTR of the AR gene, severely reducing AR expression and leading to PAIS. CONCLUSION The molecular diagnosis of PAIS remains challenging. The genomic effect of retrotransposon mobilization should be considered a possible molecular cause of AIS and other AR diseases.
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Affiliation(s)
- Rafael Loch Batista
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Hospital, Baltimore, Maryland
- Correspondence and Reprint Requests: Rafael Loch Batista, MD, PhD, Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular (LIM/42), da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, Eneas Carvalho de Aguiar, 255, 05403900 São Paulo, São Paulo, Brazil. E-mail:
| | - Katsumi Yamaguchi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Andresa di Santi Rodrigues
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mirian Yumie Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - John L Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Luciani Renata Carvalho
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Elaine M F Costa
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Haig H Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, da Disciplina de Endocrinologia e Metabologia do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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23
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Jang SM, Kauzlaric A, Quivy JP, Pontis J, Rauwel B, Coluccio A, Offner S, Duc J, Turelli P, Almouzni G, Trono D. KAP1 facilitates reinstatement of heterochromatin after DNA replication. Nucleic Acids Res 2019; 46:8788-8802. [PMID: 29955894 PMCID: PMC6158507 DOI: 10.1093/nar/gky580] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
During cell division, maintenance of chromatin features from the parental genome requires their proper establishment on its newly synthetized copy. The loss of epigenetic marks within heterochromatin, typically enriched in repetitive elements, endangers genome stability and permits chromosomal rearrangements via recombination. However, how histone modifications associated with heterochromatin are maintained across mitosis remains poorly understood. KAP1 is known to act as a scaffold for a repressor complex that mediates local heterochromatin formation, and was previously demonstrated to play an important role during DNA repair. Accordingly, we investigated a putative role for this protein in the replication of heterochromatic regions. We first found that KAP1 associates with several DNA replication factors including PCNA, MCM3 and MCM6. We then observed that these interactions are promoted by KAP1 phosphorylation on serine 473 during S phase. Finally, we could demonstrate that KAP1 forms a complex with PCNA and the histone-lysine methyltransferase Suv39h1 to reinstate heterochromatin after DNA replication.
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Affiliation(s)
- Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Benjamin Rauwel
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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24
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Puurand T, Kukuškina V, Pajuste FD, Remm M. AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mob DNA 2019; 10:31. [PMID: 31360240 PMCID: PMC6639938 DOI: 10.1186/s13100-019-0174-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
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Affiliation(s)
- Tarmo Puurand
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Viktoria Kukuškina
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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25
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Shein A, Zaikin A, Poptsova M. Recognition of 3'-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models. Sci Rep 2019; 9:7211. [PMID: 31076573 PMCID: PMC6510757 DOI: 10.1038/s41598-019-43403-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/24/2019] [Indexed: 11/09/2022] Open
Abstract
The role of 3′-end stem-loops in retrotransposition was experimentally demonstrated for transposons of various species, where LINE-SINE retrotransposons share the same 3′-end sequences, containing a stem-loop. We have discovered that 62–68% of processed pseduogenes and mRNAs also have 3′-end stem-loops. We investigated the properties of 3′-end stem-loops of human L1s, Alus, processed pseudogenes and mRNAs that do not share the same sequences, but all have 3′-end stem-loops. We have built sequence-based and structure-based machine-learning models that are able to recognize 3′-end L1, Alu, processed pseudogene and mRNA stem-loops with high performance. The sequence-based models use only sequence information and capture compositional bias in 3′-ends. The structure-based models consider physical, chemical and geometrical properties of dinucleotides composing a stem and position-specific nucleotide content of a loop and a bulge. The most important parameters include shift, tilt, rise, and hydrophilicity. The obtained results clearly point to the existence of structural constrains for 3′-end stem-loops of L1 and Alu, which are probably important for transposition, and reveal the potential of mRNAs to be recognized by the L1 machinery. The proposed approach is applicable to a broader task of recognizing RNA (DNA) secondary structures. The constructed models are freely available at github (https://github.com/AlexShein/transposons/).
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Affiliation(s)
- Alexander Shein
- Laboratory of Bioinformatics, Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Anton Zaikin
- Laboratory of Bioinformatics, Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
| | - Maria Poptsova
- Laboratory of Bioinformatics, Big Data and Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia.
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26
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Approaches and Methods for Variant Analysis in the Genome of a Single Cell. HEALTHY AGEING AND LONGEVITY 2019. [DOI: 10.1007/978-3-030-24970-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Berezovskaya F, Karev GP, Katsnelson MI, Wolf YI, Koonin EV. Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve. Biol Direct 2018; 13:27. [PMID: 30621743 PMCID: PMC6822691 DOI: 10.1186/s13062-018-0230-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Background Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer simulations suggest that emergence of genetic parasites is intrinsic to evolving replicator systems. Results Using methods of bifurcation analysis, we investigated the stability of simple models of replicator-parasite coevolution in a well-mixed environment. We first analyze what appears to be the simplest imaginable system of this type, one in which the parasite evolves during the replication of the host genome through a minimal mutation that renders the genome of the emerging parasite incapable of producing the replicase but able to recognize and recruit it for its own replication. This model has only trivial or “semi-trivial”, parasite-free equilibria: an inefficient parasite is outcompeted by the host and dies off, whereas an efficient one pushes the host out of existence, leading to the collapse of the entire system. We show that stable host-parasite coevolution (a non-trivial equilibrium) is possible in a modified model where the parasite is qualitatively distinct from the host replicator in that the replication of the parasite depends solely on the availability of the host but not on the carrying capacity of the environment. Conclusions We analytically determine the conditions for stable coevolution of genetic parasites and their hosts coevolution in simple mathematical models. It is shown that the evolutionary dynamics of a parasite that initially evolves from the host through the loss of the ability to replicate autonomously must substantially differ from that of the host, for a stable host-parasite coevolution regime to be established. Electronic supplementary material The online version of this article (10.1186/s13062-018-0230-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Faina Berezovskaya
- Department of Mathematics, Howard University, Washington, DC, 20059, USA
| | - Georgy P Karev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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28
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Tavares E, Tang CY, Vig A, Li S, Billingsley G, Sung W, Vincent A, Thiruvahindrapuram B, Héon E. Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome. Mol Genet Genomic Med 2018; 7:e00521. [PMID: 30484961 PMCID: PMC6393654 DOI: 10.1002/mgg3.521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/23/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants. Methods Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review. Results We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7‐kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements. Conclusion This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.
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Affiliation(s)
- Erika Tavares
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chen Yu Tang
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anjali Vig
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Shuning Li
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gail Billingsley
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson Sung
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ajoy Vincent
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Elise Héon
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
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29
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Klag T, Courth L, Ostaff MJ, Ott G, Stange EF, Malek NP, Seifarth W, Wehkamp J. Human Endogenous Retroviruses: Residues of Ancient Times Are Differentially Expressed in Crohn's Disease. Inflamm Intest Dis 2018; 3:125-137. [PMID: 30820434 DOI: 10.1159/000494026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/22/2018] [Indexed: 12/12/2022] Open
Abstract
Background Eight percent of the human genome consists of human endogenous retroviruses (HERV). These genetic elements are remnants of ancient retroviral germ-line infections. Altered HERV expression is associated with several chronic inflammatory diseases. A physiological role of the HERV-derived proteins syncytin-1 and -2 has been described for the integrity of the human placental cell layer in terms of maintaining feto-maternal tolerance. The aim of this project was to investigate HERV expression in Crohn's disease (CD) with a further focus on syncytins in the gut. Material and Methods Seventy-four ileal and colonic tissue samples of CD patients and healthy controls have been investigated for mRNA expression of major HERV groups by a comprehensive microarray screening. The most prominent differences have been validated by qRT-PCR. Immunohistochemistry (IHC), Western Blot (WB) and qRT-PCR were performed for syncytin-1 and -2. Results HERV microarray screening revealed a distinct expression profile in ileal and colonic tissue, as well as differential expression in CD compared to healthy controls. qRT-PCR validated differential expression of at least 3 HERV-groups in CD. qRT-PCR, IHC and WB showed a tissue-dependent diminished epithelial expression of syncytins in inflamed CD. Conclusion For the first time, HERV expression has been comprehensively studied in the gut. Between CD and healthy controls we could show a tissue dependent differential HERV expression profile. Notably, we could show that syncytin-1 and -2 are expressed in the epithelial layer in ileal and colonic tissue samples, whereas their diminished tissue-dependent expression in inflamed CD might modulate inflammatory processes at the gut barrier.
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Affiliation(s)
- Thomas Klag
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - Lioba Courth
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - Maureen J Ostaff
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - German Ott
- Department of Pathology, Robert-Bosch-Hospital, Stuttgart, Germany
| | - Eduard F Stange
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - Nisar P Malek
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - Wolfgang Seifarth
- Department of Internal Medicine III, University of Heidelberg, University Hospital Mannheim, Mannheim, Germany
| | - Jan Wehkamp
- Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
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30
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Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. Genome Biol 2018; 19:85. [PMID: 29983116 PMCID: PMC6036668 DOI: 10.1186/s13059-018-1456-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events. RESULTS Using analyses of 759 plant, fungal and animal genomes, we identify multiple possible L1 horizontal transfer events in eukaryotic species, primarily involving Tx-like L1s in marine eukaryotes. We also extend the BovB paradigm by increasing the number of estimated transfer events compared to previous studies, finding new parasite vectors of transfer such as bed bug, leech and locust, and BovB occurrences in new lineages such as bat and frog. Given that these transposable elements have colonised more than half of the genome sequence in today's mammals, our results support a role for horizontal transfer in causing long-term genomic change in new host organisms. CONCLUSIONS We describe extensive horizontal transfer of BovB retrotransposons and provide the first evidence that L1 elements can also undergo horizontal transfer. With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be a valuable resource for inferring horizontal transfer from large-scale genomic data.
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Affiliation(s)
- Atma M Ivancevic
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Neurogenetics Research Program, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - R Daniel Kortschak
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Terry Bertozzi
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - David L Adelson
- Department of Genetics and Evolution, Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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31
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Fischer CN, Campos VDA, Barella VH. On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models. J Comput Biol 2018; 25:517-527. [PMID: 29297699 DOI: 10.1089/cmb.2017.0219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class. We compared the pHMMs of all six protocols. The test results show that, for each TE superfamily, the pHMMs of at least two of the proposed protocols performed better than the conventional one and that the number of correct predictions provided by the latter can be improved by considering together the results of one or more of the alternative protocols.
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Affiliation(s)
- Carlos N Fischer
- 1 Department of Statistics, Applied Maths, and Computer Sciences, UNESP-São Paulo State University , Rio Claro, Brazil
| | - Victor De A Campos
- 2 Department of Computer Sciences, Institute of Biosciences, UNESP-São Paulo State University , São José do Rio Preto, Brazil
| | - Victor H Barella
- 3 Department of Computer Sciences, Institute of Mathematical and Computer Sciences, USP - University of São Paulo , São Carlos, Brazil
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32
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The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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33
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Bhangu JS, Taghizadeh H, Braunschmid T, Bachleitner-Hofmann T, Mannhalter C. Circulating cell-free DNA in plasma of colorectal cancer patients - A potential biomarker for tumor burden. Surg Oncol 2017; 26:395-401. [DOI: 10.1016/j.suronc.2017.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/05/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
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34
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Levy O, Knisbacher BA, Levanon EY, Havlin S. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. SCIENCE ADVANCES 2017; 3:e1701256. [PMID: 29043294 PMCID: PMC5640379 DOI: 10.1126/sciadv.1701256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/20/2017] [Indexed: 05/28/2023]
Abstract
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative "master REs" that played key roles in SVA propagation, providing strong support for the fundamental "master gene" model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes.
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Affiliation(s)
- Orr Levy
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Binyamin A. Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Erez Y. Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shlomo Havlin
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
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35
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Navarrete HP, Soler LH, Mares RE, Ramos MA. Frequency of Alu insertions within the ACE and PR loci in Northwestern Mexicans. BMC Res Notes 2017; 10:339. [PMID: 28750672 PMCID: PMC5530943 DOI: 10.1186/s13104-017-2673-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 07/22/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Presently, non-LTR retrotransposons are the most active mobile elements in the human genome. Among these, Alu elements are highly represented in the modern population. Worldwide, distribution of Alu polymorphisms (insertion/deletion; I/D) shows variability between different populations. Two Alu insertion loci, ACE and PR, are significant biomarkers that have served in several genotype-phenotype association studies. In Mexico, studies concerning the frequency of these biomarkers have been conducted mainly in subpopulations from central and southern regions. Here, we screened a population sample of the northwestern region to gain further knowledge regarding the prevalence of Alu polymorphisms within ACE and PR loci. RESULTS For ACE locus, the observed genotype frequencies were 26.5, 51.0 and 22.5% for II, ID, and DD, respectively; and allelic frequencies for I and D were 52 and 48%. Whereas respective genotype frequencies for PR locus were 2.7, 26.5 and 70.8%, and the corresponding allele frequencies were 16 and 84%. Furthermore, the insertion frequency within ACE locus was similar between central, western and northwestern subpopulations, and rather higher in southeastern subpopulation (p < 0.05). Although the occurrence of Alu polymorphisms within PR locus has not been widely examined, the insertion frequency was higher in northwestern subpopulation, as compared with western and southeastern subpopulations (p < 0.05). Based on the frequency of Alu insertions found in ACE and PR loci, subpopulations from the northwestern, western and central regions share a common genetic origin, but apparently not with the subpopulation from the southeastern region, in accordance with the notion that assumes the existence of a broad genomic diversity in the Mexican population. In addition, the high prevalence of Alu insertions reveals their potential application as biomarkers with prognostic value for the associated diseases; e.g., as part of the standard protocols for clinical diagnosis.
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Affiliation(s)
- Hilda P Navarrete
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Linda H Soler
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Rosa E Mares
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Marco A Ramos
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico.
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36
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Treiber CD, Waddell S. Resolving the prevalence of somatic transposition in Drosophila. eLife 2017; 6. [PMID: 28742021 PMCID: PMC5553932 DOI: 10.7554/elife.28297] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/21/2017] [Indexed: 11/13/2022] Open
Abstract
Somatic transposition in mammals and insects could increase cellular diversity and neural mobilization has been implicated in age-dependent decline. To understand the impact of transposition in somatic cells it is essential to reliably measure the frequency and map locations of new insertions. Here we identified thousands of putative somatic transposon insertions in neurons from individual Drosophila melanogaster using whole-genome sequencing. However, the number of de novo insertions did not correlate with transposon expression or fly age. Analysing our data with exons as 'immobile genetic elements' revealed a similar frequency of unexpected exon translocations. A new sequencing strategy that recovers transposon: chromosome junction information revealed most putative de novo transposon and exon insertions likely result from unavoidable chimeric artefacts. Reanalysis of other published data suggests similar artefacts are often mistaken for genuine somatic transposition. We conclude that somatic transposition is less prevalent in Drosophila than previously envisaged.
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Affiliation(s)
- Christoph D Treiber
- Centre for Neural Circuits and Behaviour, The University of Oxford, Oxford, United Kingdom
| | - Scott Waddell
- Centre for Neural Circuits and Behaviour, The University of Oxford, Oxford, United Kingdom
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37
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Chernyavskaya Y, Mudbhary R, Zhang C, Tokarz D, Jacob V, Gopinath S, Sun X, Wang S, Magnani E, Madakashira BP, Yoder JA, Hoshida Y, Sadler KC. Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling. Development 2017; 144:2925-2939. [PMID: 28698226 DOI: 10.1242/dev.147629] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/02/2017] [Indexed: 12/19/2022]
Abstract
Complex cytoplasmic nucleotide-sensing mechanisms can recognize foreign DNA based on a lack of methylation and initiate an immune response to clear the infection. Zebrafish embryos with global DNA hypomethylation caused by mutations in the ubiquitin-like with PHD and ring finger domains 1 (uhrf1) or DNA methyltransferase 1 (dnmt1) genes exhibit a robust interferon induction characteristic of the first line of defense against viral infection. We found that this interferon induction occurred in non-immune cells and examined whether intracellular viral sensing pathways in these cells were the trigger. RNA-seq analysis of uhrf1 and dnmt1 mutants revealed widespread induction of Class I retrotransposons and activation of cytoplasmic DNA viral sensors. Attenuating Sting, phosphorylated Tbk1 and, importantly, blocking reverse transcriptase activity suppressed the expression of interferon genes in uhrf1 mutants. Thus, activation of transposons in cells with global DNA hypomethylation mimics a viral infection by activating cytoplasmic DNA sensors. This suggests that antiviral pathways serve as surveillance of cells that have derepressed intragenomic parasites due to DNA hypomethylation.
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Affiliation(s)
- Yelena Chernyavskaya
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raksha Mudbhary
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Chi Zhang
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Debra Tokarz
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27607, USA
| | - Vinitha Jacob
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Smita Gopinath
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Xiaochen Sun
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Shuang Wang
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Elena Magnani
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC 27607, USA
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Kirsten C Sadler
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA.,Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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38
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Santander CG, Gambron P, Marchi E, Karamitros T, Katzourakis A, Magiorkinis G. STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data. Virus Evol 2017; 3:vex023. [PMID: 28948042 PMCID: PMC5597868 DOI: 10.1093/ve/vex023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The advancements of high-throughput genomics have unveiled much about the human genome highlighting the importance of variations between individuals and their contribution to disease. Even though numerous software have been developed to make sense of large genomics datasets, a major short falling of these has been the inability to cope with repetitive regions, specifically to validate structural variants and accordingly assess their role in disease. Here we describe our program STEAK, a massively parallel software designed to detect chimeric reads in high-throughput sequencing data for a broad number of applications such as identifying presence/absence, as well as discovery of transposable elements (TEs), and retroviral integrations. We highlight the capabilities of STEAK by comparing its efficacy in locating HERV-K HML-2 in clinical whole genome projects, target enrichment sequences, and in the 1000 Genomes CEU Trio to the performance of other TE and virus detecting tools. We show that STEAK outperforms other software in terms of computational efficiency, sensitivity, and specificity. We demonstrate that STEAK is a robust tool, which allows analysts to flexibly detect and evaluate TE and retroviral integrations in a diverse range of sequencing projects for both research and clinical purposes.
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Affiliation(s)
| | - Philippe Gambron
- Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Emanuele Marchi
- Nuffield Department of Medicine, University of Oxford, Oxfordshire, UK
| | | | | | - Gkikas Magiorkinis
- Department of Zoology, University of Oxford, Oxfordshire, UK
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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39
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Intragenic multi-exon deletion in the FBN1 gene in a child with mildly dilated aortic sinus: a retrotransposal event. J Hum Genet 2017; 62:711-715. [PMID: 28331219 DOI: 10.1038/jhg.2017.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/08/2022]
Abstract
Marfan syndrome is an autosomal dominant disorder affecting mainly the skeletal, ocular and cardiovascular systems. Most cases are caused by mutations in the fibrillin-1 gene (FBN1), although there are some reports on deletions involving FBN1 and other additional genes. We report a male patient who was first evaluated at 4 years of age. Echocardiogram showed a mildly dilated aortic sinus. He also had a history of muscular ventral septal defect which was closed spontaneously and trivial mitral regurgitation. Other phenotypic features include frontal bossing, anteverted ears, joint hyperlaxity, learning disability, skin striae, and height and weight in the >97th centile but no other diagnostic findings of MFS and does not fulfill the revised Ghent criteria. Chromosomal microarray analysis showed a deletion of approximately 36.8 kb at 15q21.1, which starts in intron 6 and ends in intron 9 and includes three FBN1 exons. Sequence analysis of the breakpoint region confirmed the deletion and revealed a concomitant insertion of a retrotransposon within the intron 6/intron 9 region. The intragenic deletion of exons 7-9 was likely the result of a retrotransposition event by a MAST2-SVA element mediated by repetitive sequences.
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40
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Wang L, Rishishwar L, Mariño-Ramírez L, Jordan IK. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. Nucleic Acids Res 2017; 45:2318-2328. [PMID: 27998931 PMCID: PMC5389732 DOI: 10.1093/nar/gkw1286] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023] Open
Abstract
Transposable element (TE) derived sequences are known to contribute to the regulation of the human genome. The majority of known TE-derived regulatory sequences correspond to relatively ancient insertions, which are fixed across human populations. The extent to which human genetic variation caused by recent TE activity leads to regulatory polymorphisms among populations has yet to be thoroughly explored. In this study, we searched for associations between polymorphic TE (polyTE) loci and human gene expression levels using an expression quantitative trait loci (eQTL) approach. We compared locus-specific polyTE insertion genotypes to B cell gene expression levels among 445 individuals from 5 human populations. Numerous human polyTE loci correspond to both cis and trans eQTL, and their regulatory effects are directly related to cell type-specific function in the immune system. PolyTE loci are associated with differences in expression between European and African population groups, and a single polyTE loci is indirectly associated with the expression of numerous genes via the regulation of the B cell-specific transcription factor PAX5. The polyTE-gene expression associations we found indicate that human TE genetic variation can have important phenotypic consequences. Our results reveal that TE-eQTL are involved in population-specific gene regulation as well as transcriptional network modification.
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Affiliation(s)
- Lu Wang
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Applied Bioinformatics Laboratory, Atlanta, GA 30332, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, 760043, Colombia
- BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, 170002, Colombia
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, 760043, Colombia
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - I. King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Applied Bioinformatics Laboratory, Atlanta, GA 30332, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, 760043, Colombia
- BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, 170002, Colombia
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41
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Clayton EA, Wang L, Rishishwar L, Wang J, McDonald JF, Jordan IK. Patterns of Transposable Element Expression and Insertion in Cancer. Front Mol Biosci 2016; 3:76. [PMID: 27900322 PMCID: PMC5110550 DOI: 10.3389/fmolb.2016.00076] [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: 08/24/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data. We applied these new sequence analysis techniques to matched normal and primary tumor patient samples from the Cancer Genome Atlas (TCGA) in order to analyze the patterns of TE expression and insertion for three cancer types: breast invasive carcinoma, head and neck squamous cell carcinoma, and lung adenocarcinoma. Our analysis focused on the three most abundant families of active human TEs: Alu, SVA, and L1. We found evidence for high levels of somatic TE activity for these three families in normal and cancer samples across diverse tissue types. Abundant transcripts for all three TE families were detected in both normal and cancer tissues along with an average of ~80 unique TE insertions per individual patient/tissue. We observed an increase in L1 transcript expression and L1 insertional activity in primary tumor samples for all three cancer types. Tumor-specific TE insertions are enriched for private mutations, consistent with a potentially causal role in tumorigenesis. We used genome feature analysis to investigate two specific cases of putative cancer-causing TE mutations in further detail. An Alu insertion in an upstream enhancer of the CBL tumor suppressor gene is associated with down-regulation of the gene in a single breast cancer patient, and an L1 insertion in the first exon of the BAALC gene also disrupts its expression in head and neck squamous cell carcinoma. Our results are consistent with widespread somatic activity of human TEs leading to numerous insertion mutations that can contribute to tumorigenesis in a variety of tissues.
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Affiliation(s)
- Evan A Clayton
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - Lu Wang
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University East Lansing, MI, USA
| | - John F McDonald
- Integrated Cancer Research Center, School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; Ovarian Cancer InstituteAtlanta, GA, USA
| | - I King Jordan
- School of Biology, Georgia Institute of TechnologyAtlanta, GA, USA; PanAmerican Bioinformatics InstituteCali, Colombia; Applied Bioinformatics LaboratoryAtlanta, GA, USA
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42
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Nascimento FF, Rodrigo AG. Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution. PLoS One 2016; 11:e0162454. [PMID: 27649303 PMCID: PMC5029938 DOI: 10.1371/journal.pone.0162454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/02/2016] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy. In TM, any element of a given family is able to replicate in the host genome. In this paper, we simulated ERV phylogenetic trees under variations of SMM and TM. To test whether current phylogenetic programs can recover the simulated ERV phylogenies, DNA sequence alignments were simulated and maximum likelihood trees were reconstructed and compared to the simulated phylogenies. Results indicate that visual inspection of phylogenetic trees alone can be misleading. However, if a set of statistical summaries is calculated, we are able to distinguish between models with high accuracy by using a data mining algorithm that we introduce here. We also demonstrate the use of our data mining algorithm with empirical data for the porcine endogenous retrovirus (PERV), an ERV that is able to replicate in human and pig cells in vitro.
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Affiliation(s)
| | - Allen G. Rodrigo
- National Evolutionary Synthesis Center, Durham, NC, United States of America
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43
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Du C, Pusey BN, Adams CJ, Lau CC, Bone WP, Gahl WA, Markello TC, Adams DR. Explorations to improve the completeness of exome sequencing. BMC Med Genomics 2016; 9:56. [PMID: 27568008 PMCID: PMC5002202 DOI: 10.1186/s12920-016-0216-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 08/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis. Such false negatives reflect limitations in experimental design, technical performance, and data analysis. RESULTS We present examples from our datasets to quantify the analytical performance associated with current practices, and explore strategies to improve the completeness of data analysis. In particular, we focus on patient ascertainment, exome capture, inclusion of intronic variants, and evaluation of medium-sized structural variants. CONCLUSIONS The strategies we present may recover previously-missed, disease causing variants in second-pass exome analysis. Understanding the limitations of the current clinical exome search space provides a rational basis to improve methods for disease variant detection using genome-scale sequencing techniques.
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Affiliation(s)
- Chen Du
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Christopher J Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - C Christopher Lau
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William P Bone
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA.
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44
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Śliwińska EB, Martyka R, Tryjanowski P. Evolutionary interaction between W/Y chromosome and transposable elements. Genetica 2016; 144:267-78. [PMID: 27000053 PMCID: PMC4879163 DOI: 10.1007/s10709-016-9895-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 03/13/2016] [Indexed: 11/28/2022]
Abstract
The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.
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Affiliation(s)
- Ewa B Śliwińska
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland.
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland.
| | - Rafał Martyka
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120, Kraków, Poland
| | - Piotr Tryjanowski
- Institute of Zoology, Poznań University of Life Sciences, Wojska Polskiego 71C, 60-625, Poznań, Poland
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45
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Mulero-Navarro S, Fernandez-Salguero PM. New Trends in Aryl Hydrocarbon Receptor Biology. Front Cell Dev Biol 2016; 4:45. [PMID: 27243009 PMCID: PMC4863130 DOI: 10.3389/fcell.2016.00045] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/28/2016] [Indexed: 12/28/2022] Open
Abstract
Traditionally considered as a critical intermediate in the toxic and carcinogenic response to dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD), the Aryl hydrocarbon/Dioxin receptor (AhR) has proven to be also an important regulator of cell physiology and organ homeostasis. AhR has become an interesting and actual area of research mainly boosted by a significant number of recent studies analyzing its contribution to the proper functioning of the immune, hepatic, cardiovascular, vascular and reproductive systems. At the cellular level, AhR establishes functional interactions with signaling pathways governing cell proliferation and cell cycle, cell morphology, cell adhesion and cell migration. Two exciting new aspects in AhR biology deal with its implication in the control of cell differentiation and its more than likely involvement in cell pluripotency and stemness. In fact, it is possible that AhR could help modulate the balance between differentiation and pluripotency in normal and transformed tumor cells. At the molecular level, AhR regulates an increasingly large array of physiologically relevant genes either by traditional transcription-dependent mechanisms or by unforeseen processes involving genomic insulators, chromatin dynamics and the transcription of mobile genetic elements. AhR is also closely related to epigenetics, not only from the point of view of target gene expression but also with respect to its own regulation by promoter methylation. It is reasonable to consider that deregulation of these many functions could have a causative role, or at least contribute to, human disease. Consequently, several laboratories have proposed that AhR could be a valuable tool as diagnostic marker and/or therapeutic target in human pathologies. An additional point of interest is the possibility of regulating AhR activity by endogenous non-toxic low weight molecules agonist or antagonist molecules that could be present or included in the diet. In this review, we will address these molecular and functional features of AhR biology within physiological and pathological contexts.
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Affiliation(s)
- Sonia Mulero-Navarro
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura Badajoz, Spain
| | - Pedro M Fernandez-Salguero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura Badajoz, Spain
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46
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Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome. J Mol Biol 2016; 428:658-667. [PMID: 26780549 DOI: 10.1016/j.jmb.2016.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Holliday junctions (HJs) constitute important intermediate structures for many cell functions such as DNA recombination and DNA repair. They derive from a 10-nt degenerate sequence, with a 3-nt core motif. In this study, we explored the human genome whether the HJ degenerate sequence associates with transposable elements (TEs) and mainly with those of the active and inactive ALU, LINE, SVA and HERV families. We identified six different forms of the HJ sequence motif, and we located the genomic coordinates of sequences containing both HJs and TEs. From 2982 total HJs, a significant number of 1319 TE-associated HJs were found, with a median distribution of 1 per 2.4 Mb. The HJs with higher GC content were observed more frequently at the genome. A high percentage of HJs were associated with all main TE families, with specificity for particular active or inactive elements: DNA elements and the retroelements ALUs, LINEs and HERVs up to 41.94%, 72.72%, 42.94% and 84.5%, respectively. Phylogenetic analysis revealed that HJs occur in both active and inactive TEs. Furthermore, the TE-associated HJs were almost exclusively found within a distance less than 1 Mb from human genes, while only 23 were not associated with any genes. This is the first report associating human HJs, with mobile elements. Our data pinpoint that particular HJ forms show preference for specific active retrotransposon families of ALUs and LINEs, suggesting that retrotransposon-incorporated HJs may relocate or replicate in the genome through retrotransposition, contributing to recombination, genome plasticity and DNA repair.
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47
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Mita P, Boeke JD. How retrotransposons shape genome regulation. Curr Opin Genet Dev 2016; 37:90-100. [PMID: 26855260 DOI: 10.1016/j.gde.2016.01.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/30/2015] [Accepted: 01/17/2016] [Indexed: 12/30/2022]
Abstract
Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA.
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA
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48
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Lapp HE, Hunter RG. The dynamic genome: transposons and environmental adaptation in the nervous system. Epigenomics 2016; 8:237-49. [DOI: 10.2217/epi.15.107] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Classically thought as genomic clutter, the functional significance of transposable elements (TEs) has only recently become a focus of attention in neuroscience. Increasingly, studies have demonstrated that the brain seems to have more retrotransposition and TE transcription relative to other somatic tissues, suggesting a unique role for TEs in the central nervous system. TE expression and transposition also appear to vary by brain region and change in response to environmental stimuli such as stress. TEs appear to serve a number of adaptive roles in the nervous system. The regulation of TE expression by steroid, epigenetic and other mechanisms in interplay with the environment represents a significant and novel avenue to understanding both normal brain function and disease.
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Affiliation(s)
- Hannah E Lapp
- Department of Psychology & Developmental Brain Sciences Program, University of Massachusetts Boston, Boston, MA 02125-3393, USA
| | - Richard G Hunter
- Department of Psychology & Developmental Brain Sciences Program, University of Massachusetts Boston, Boston, MA 02125-3393, USA
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49
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Wildschutte JH, Baron A, Diroff NM, Kidd JM. Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res 2015; 43:10292-307. [PMID: 26503250 PMCID: PMC4666360 DOI: 10.1093/nar/gkv1089] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/08/2015] [Indexed: 12/03/2022] Open
Abstract
Alu insertions have contributed to >11% of the human genome and ∼30–35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5′ truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5′ truncations. Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.
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Affiliation(s)
- Julia H Wildschutte
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alayna Baron
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicolette M Diroff
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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50
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Hoen DR, Hickey G, Bourque G, Casacuberta J, Cordaux R, Feschotte C, Fiston-Lavier AS, Hua-Van A, Hubley R, Kapusta A, Lerat E, Maumus F, Pollock DD, Quesneville H, Smit A, Wheeler TJ, Bureau TE, Blanchette M. A call for benchmarking transposable element annotation methods. Mob DNA 2015; 6:13. [PMID: 26244060 PMCID: PMC4524446 DOI: 10.1186/s13100-015-0044-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022] Open
Abstract
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.
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Affiliation(s)
- Douglas R Hoen
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Glenn Hickey
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec Canada ; McGill University and Génome Québec Innovation Center, Montréal, Québec Canada
| | - Josep Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR5554 CNRS-Université Montpellier, Montpellier, 34090 cedex 05 France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes, Comportement Ecologie, CNRS-Université Paris-Sud (UMR 9191)-IRD (UMR 247)-Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Robert Hubley
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
| | - Emmanuelle Lerat
- Laboratoire Biometrie et Biologie Evolutive, Universite Claude Bernard-Lyon 1, UMR-CNRS 5558-Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - David D Pollock
- University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France
| | - Arian Smit
- Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA
| | - Travis J Wheeler
- Department of Computer Science, University of Montana, Missoula, MT 59812 USA
| | - Thomas E Bureau
- Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada
| | - Mathieu Blanchette
- School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada
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