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Drobyshev A, Modestov A, Suntsova M, Poddubskaya E, Seryakov A, Moisseev A, Sorokin M, Tkachev V, Zakharova G, Simonov A, Zolotovskaia MA, Buzdin A. Pan-cancer experimental characteristic of human transcriptional patterns connected with telomerase reverse transcriptase ( TERT) gene expression status. Front Genet 2024; 15:1401100. [PMID: 38859942 PMCID: PMC11163056 DOI: 10.3389/fgene.2024.1401100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/08/2024] [Indexed: 06/12/2024] Open
Abstract
The TERT gene encodes the reverse transcriptase subunit of telomerase and is normally transcriptionally suppressed in differentiated human cells but reactivated in cancers where its expression is frequently associated with poor survival prognosis. Here we experimentally assessed the RNA sequencing expression patterns associated with TERT transcription in 1039 human cancer samples of 27 tumor types. We observed a bimodal distribution of TERT expression where ∼27% of cancer samples did not express TERT and the rest showed a bell-shaped distribution. Expression of TERT strongly correlated with 1443 human genes including 103 encoding transcriptional factor proteins. Comparison of TERT- positive and negative cancers showed the differential activation of 496 genes and 1975 molecular pathways. Therein, 32/38 (84%) of DNA repair pathways were hyperactivated in TERT+ cancers which was also connected with accelerated replication, transcription, translation, and cell cycle progression. In contrast, the level of 40 positive cell cycle regulator proteins and a set of epithelial-to-mesenchymal transition pathways was specific for the TERT- group suggesting different proliferation strategies for both groups of cancer. Our pilot study showed that the TERT+ group had ∼13% of cancers with C228T or C250T mutated TERT promoter. However, the presence of promoter mutations was not associated with greater TERT expression compared with other TERT+ cancers, suggesting parallel mechanisms of its transcriptional activation in cancers. In addition, we detected a decreased expression of L1 retrotransposons in the TERT+ group, and further decreased L1 expression in promoter mutated TERT+ cancers. TERT expression was correlated with 17 genes encoding molecular targets of cancer therapeutics and may relate to differential survival patterns of TERT- positive and negative cancers.
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Affiliation(s)
- Aleksey Drobyshev
- Endocrinology Research Center, Moscow, Russia
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexander Modestov
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria Suntsova
- Endocrinology Research Center, Moscow, Russia
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Elena Poddubskaya
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
- Clinical Center Vitamed, Moscow, Russia
| | | | - Aleksey Moisseev
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maksim Sorokin
- Endocrinology Research Center, Moscow, Russia
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Galina Zakharova
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aleksander Simonov
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Endocrinology Research Center, Moscow, Russia
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Center for Advanced Studies 20, Moscow, Russia
| | - Anton Buzdin
- Endocrinology Research Center, Moscow, Russia
- Institute of Personalized Oncology, I. M. Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Center for Advanced Studies 20, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Suntsova MV, Buzdin AA. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics 2020; 21:535. [PMID: 32912141 PMCID: PMC7488140 DOI: 10.1186/s12864-020-06962-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5-7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species.
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Affiliation(s)
- Maria V Suntsova
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia
| | - Anton A Buzdin
- Institute for personalized medicine, I.M. Sechenov First Moscow State Medical University, Trubetskaya 8, Moscow, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, Russia. .,Omicsway Corp, Walnut, CA, USA. .,Moscow Institute of Physics and Technology (National Research University), 141700, Moscow, Russia.
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3
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Krenzien F, Katou S, Papa A, Sinn B, Benzing C, Feldbrügge L, Kamali C, Brunnbauer P, Splith K, Lorenz RR, Ritschl P, Wiering L, Öllinger R, Schöning W, Pratschke J, Schmelzle M. Increased Cell-Free DNA Plasma Concentration Following Liver Transplantation Is Linked to Portal Hepatitis and Inferior Survival. J Clin Med 2020; 9:jcm9051543. [PMID: 32443763 PMCID: PMC7291032 DOI: 10.3390/jcm9051543] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/15/2022] Open
Abstract
Donor organ quality is crucial for transplant survival and long-term survival of patients after liver transplantation. Besides bacterial and viral infections, endogenous damage-associated molecular patterns (DAMPs) can stimulate immune responses. Cell-free DNA (cfDNA) is one such DAMP that exhibits highly proinflammatory effects via DNA sensors. Herein, we measured cfDNA after liver transplantation and found elevated levels when organs from resuscitated donors were transplanted. High levels of cfDNA were associated with high C-reactive protein, leukocytosis as well as granulocytosis in the recipient. In addition to increased systemic immune responses, portal hepatitis was observed, which was associated with increased interface activity and a higher numbers of infiltrating neutrophils and eosinophils in the graft. In fact, the cfDNA was an independent significant factor in multivariate analysis and increased concentration of cfDNA was associated with inferior 1-year survival. Moreover, cfDNA levels were found to be decreased significantly during the postoperative course when patients underwent continuous veno-venous haemofiltration. In conclusion, patients receiving livers from resuscitated donors were characterised by high postoperative cfDNA levels. Those patients showed pronounced portal hepatitis and systemic inflammatory responses in the short term leading to a high mortality. Further studies are needed to evaluate the clinical relevance of cfDNA clearance by haemoadsorption and haemofiltration in vitro and in vivo.
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Affiliation(s)
- Felix Krenzien
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Shadi Katou
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Alba Papa
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Bruno Sinn
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
- Institute of Pathology, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Christian Benzing
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Linda Feldbrügge
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Can Kamali
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Philipp Brunnbauer
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Katrin Splith
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Ralf Roland Lorenz
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Paul Ritschl
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Leke Wiering
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Robert Öllinger
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Wenzel Schöning
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Johann Pratschke
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
| | - Moritz Schmelzle
- Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, Charité—Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 13353 Berlin, Germany; (F.K.); (A.P.); (C.B.); (L.F.); (C.K.); (P.B.); (K.S.); (R.R.L.); (P.R.); (L.W.); (R.Ö.); (W.S.); (J.P.)
- Berlin Institute of Health (BIH), 10178 Berlin, Germany;
- Correspondence:
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4
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Breitbach S, Tug S, Helmig S, Zahn D, Kubiak T, Michal M, Gori T, Ehlert T, Beiter T, Simon P. Direct quantification of cell-free, circulating DNA from unpurified plasma. PLoS One 2014; 9:e87838. [PMID: 24595313 PMCID: PMC3940427 DOI: 10.1371/journal.pone.0087838] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/30/2013] [Indexed: 02/06/2023] Open
Abstract
Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical medicine and other research fields. In this article we provide a direct quantitative real-time PCR (qPCR) as a sensitive tool for the measurement of cfDNA from plasma without previous DNA extraction, which is known to be accompanied by a reduction of DNA yield. The primer sets were designed to amplify a 90 and 222 bp multi-locus L1PA2 sequence. In the first module, cfDNA concentrations in unpurified plasma were compared to cfDNA concentrations in the eluate and the flow-through of the QIAamp DNA Blood Mini Kit and in the eluate of a phenol-chloroform isoamyl (PCI) based DNA extraction, to elucidate the DNA losses during extraction. The analyses revealed 2.79-fold higher cfDNA concentrations in unpurified plasma compared to the eluate of the QIAamp DNA Blood Mini Kit, while 36.7% of the total cfDNA were found in the flow-through. The PCI procedure only performed well on samples with high cfDNA concentrations, showing 87.4% of the concentrations measured in plasma. The DNA integrity strongly depended on the sample treatment. Further qualitative analyses indicated differing fractions of cfDNA fragment lengths in the eluate of both extraction methods. In the second module, cfDNA concentrations in the plasma of 74 coronary heart disease patients were compared to cfDNA concentrations of 74 healthy controls, using the direct L1PA2 qPCR for cfDNA quantification. The patient collective showed significantly higher cfDNA levels (mean (SD) 20.1 (23.8) ng/ml; range 5.1–183.0 ng/ml) compared to the healthy controls (9.7 (4.2) ng/ml; range 1.6–23.7 ng/ml). With our direct qPCR, we recommend a simple, economic and sensitive procedure for the quantification of cfDNA concentrations from plasma that might find broad applicability, if cfDNA became an established marker in the assessment of pathophysiological conditions.
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Affiliation(s)
- Sarah Breitbach
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Suzan Tug
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Daniela Zahn
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Kubiak
- Department of Health Psychology, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Matthias Michal
- Department of Psychosomatic Medicine and Psychotherapy, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tommaso Gori
- Department of Cardiology, Angiology and Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Thomas Beiter
- Department of Sports Medicine, Medical Clinic, Eberhard-Karls-University of Tuebingen, Tuebingen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Prevention, Johannes Gutenberg-University of Mainz, Mainz, Germany
- * E-mail:
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5
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Abstract
Type 1 long-interspersed nuclear elements (L1s) are autonomous retrotransposable elements that retain the potential for activity in the human genome but are suppressed by host factors. Retrotransposition of L1s into chromosomal DNA can lead to genomic instability, whereas reverse transcription of L1 in the cytosol has the potential to activate innate immune sensors. We hypothesized that HIV-1 infection would compromise cellular control of L1 elements, resulting in the induction of retrotransposition events. Here, we show that HIV-1 infection enhances L1 retrotransposition in Jurkat cells in a Vif- and Vpr-dependent manner. In primary CD4(+) cells, HIV-1 infection results in the accumulation of L1 DNA, at least the majority of which is extrachromosomal. These data expose an unrecognized interaction between HIV-1 and endogenous retrotransposable elements, which may have implications for the innate immune response to HIV-1 infection, as well as for HIV-1-induced genomic instability and cytopathicity.
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6
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Abstract
Mobile DNAs have had a central role in shaping our genome. More than half of our DNA is comprised of interspersed repeats resulting from replicative copy and paste events of retrotransposons. Although most are fixed, incapable of templating new copies, there are important exceptions to retrotransposon quiescence. De novo insertions cause genetic diseases and cancers, though reliably detecting these occurrences has been difficult. New technologies aimed at uncovering polymorphic insertions reveal that mobile DNAs provide a substantial and dynamic source of structural variation. Key questions going forward include how and how much new transposition events affect human health and disease.
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Affiliation(s)
- Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Price EM, Cotton AM, Peñaherrera MS, McFadden DE, Kobor MS, Robinson W. Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues. Epigenetics 2012; 7:652-63. [PMID: 22531475 PMCID: PMC3398992 DOI: 10.4161/epi.20221] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA methylation of CpGs located in two types of repetitive elements-LINE1 (L1) and Alu-is used to assess "global" changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.
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Affiliation(s)
- E Magda Price
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
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Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 2011; 12:187-215. [PMID: 21801021 DOI: 10.1146/annurev-genom-082509-141802] [Citation(s) in RCA: 394] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes.
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Affiliation(s)
- Christine R Beck
- Department of Human Genetics, University of MIchigan Medical School, Ann Arbor, Michigan 48109-5618, USA.
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9
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Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 2010; 11:410. [PMID: 20591181 PMCID: PMC2996938 DOI: 10.1186/1471-2164-11-410] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/30/2010] [Indexed: 11/10/2022] Open
Abstract
Background Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals. Results Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human AluYb8 and AluYb9 subfamilies. In four individuals, we identified a total of 2,758 AluYb8 and AluYb9 insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%. Conclusions Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.
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Affiliation(s)
- David J Witherspoon
- Dept. of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA.
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Ewing AD, Kazazian HH. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 2010; 20:1262-70. [PMID: 20488934 DOI: 10.1101/gr.106419.110] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome. Using diagnostic nucleotides, we were able to locate the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements. We find that any two individual genomes differ at an average of 285 sites with respect to L1 insertion presence or absence. In total, we assayed 25 individuals, 15 of which are unrelated, at 1139 sites, including 772 shared with the reference genome and 367 nonreference L1 insertions. We show that L1Hs profiles recapitulate genetic ancestry, and determine the chromosomal distribution of these elements. Using these data, we estimate that the rate of L1 retrotransposition in humans is between 1/95 and 1/270 births, and the number of dimorphic L1 elements in the human population with gene frequencies greater than 0.05 is between 3000 and 10,000.
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Affiliation(s)
- Adam D Ewing
- University of Pennsylvania Department of Genetics, Philadelphia, Pennsylvania 19104, USA
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11
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Buzdin AA. [Functional analysis of retroviral endogenous inserts in the human genome evolution]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:38-46. [PMID: 20386577 DOI: 10.1134/s1068162010010048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Retroelements, mobile elements produced in DNA by reverse transcription, comprise about 40% of the human genome. A small part of these elements appeared in the genome quite recently after the divergence of humans and chimpanzees had occurred. Evolutionarily young retroelements are represented by the members of four groups, SVA, Alu, L1, and the endogenous HERV-K (HML-2) virus. These retroelements could play a functional role in the course of the molecular evolution of human DNA. We comprehensively studied the contribution of human-specific endogenous viruses (hsERV) to the structural modifications and regulation of the human genome. We found that hsERV presented in 134 copies occupied about 330 000 bp of human DNA. They added to genomic sequences the copies of 50 functional retroviral genes as well as 134 potential promoters and enhancers, 50% of which are located in the regions adjacent to known genes, and 22% in gene introns. At least 67% of these elements are human-specific promoters in vivo. hsERV viruses regulate the activity of known protein-encoding genes by means of RNA interference, function as enhancers, and provide new polyadenylation signals for mRNA.
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Amosova AL, Komkov AI, Ustiugova SV, Mamedov IZ, Lebedev IB. [Retroposons in modern human genome evolution]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 35:779-88. [PMID: 20208577 DOI: 10.1134/s1068162009060053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The ascertainment of the rates and driving forces of human genome evolution along with the genetic diversity of populations or separate population groups remains a topical problem of fundamental and applied genomics. According to the results of comparative analysis, the most numerous human genome structure peculiarities are connected with the distribution of mobile genetic retroelements - LTR, LINE1, SVA, and Alu repeats. Due to the wide distribution in different genome loci, conversed retropositional activity, and the retroelements regulatory potential, let us regard them as one of the significant evolutionary driving forces and the source of human genome variability. In the current review, we summarize published data and recent results of our research aimed at the analysis of the evolutionary impact of the young retroelements group on the function and variability of the human genome. We examine modern approaches of the polygenomic identification of polymorphic retroelements inserts. Using an original Internet resource, we analyze special features of the genomic polymorphic inserts of Alu repeats. We thoroughly characterize the strategy of large-scale functional analysis of polymorphic retroelement inserts. The presented results confirm the hypothesis of the roles of retroelements as active cis regulatory elements that are able to modulate surrounding genes.
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Mamedov IZ, Amosova AL, Fisunov GY, Lebedev YB. A new polymorphic retroelement database (PRED) for the human genome. Mol Biol 2008. [DOI: 10.1134/s0026893308040213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Takabatake T, Ishihara H, Ohmachi Y, Tanaka I, Nakamura MM, Fujikawa K, Hirouchi T, Kakinuma S, Shimada Y, Oghiso Y, Tanaka K. Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome. Nucleic Acids Res 2008; 36:e59. [PMID: 18450814 PMCID: PMC2425471 DOI: 10.1093/nar/gkn235] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mammalian genomes contain numerous evolutionary harbored mobile elements, a part of which are still active and may cause genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression or disruption of neighboring host genes. Here, we describe a novel microarray-based method by which dispersed genomic locations of a type of retrotransposon in a mammalian genome can be identified. Using this method, we mapped the DNA elements for a mouse retrotransposon, intracisternal A-particle (IAP), within genomes of C3H/He and C57BL/6J inbred mouse strains; consequently we detected hundreds of probable IAP cDNA-integrated genomic regions, in which a considerable number of strain-specific putative insertions were included. In addition, by comparing genomic DNAs from radiation-induced myeloid leukemia cells and its reference normal tissue, we detected three genomic regions around which an IAP element was integrated. These results demonstrate the first successful genome-wide mapping of a retrotransposon type in a mammalian genome.
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Affiliation(s)
- Takashi Takabatake
- Department of Radiobiology, Institute for Environmental Sciences, 2-121, Hacchazawa, Takahoko, Rokkasho, Aomori 039-3213, Japan.
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15
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Sen SK, Huang CT, Han K, Batzer MA. Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. Nucleic Acids Res 2007; 35:3741-51. [PMID: 17517773 PMCID: PMC1920257 DOI: 10.1093/nar/gkm317] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising approximately 17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and characterized 21 loci where L1 elements have integrated without signs of endonuclease-related activity. The structural features of these loci suggest a role for this process in DNA double-strand break repair. We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA.
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Affiliation(s)
| | | | | | - Mark A. Batzer
- *To whom correspondence should be addressed. +1 225 578 7102+1 225 578 7113
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Ustyugova SV, Lebedev YB, Sverdlov ED. Long L1 insertions in human gene introns specifically reduce the content of corresponding primary transcripts. Genetica 2007; 128:261-72. [PMID: 17028956 DOI: 10.1007/s10709-005-5967-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 12/15/2005] [Indexed: 10/24/2022]
Abstract
LINE-1 (L1) retrotransposons comprise about 17% of the human genome and include a recently transposed set of Ta-L1 elements that are polymorphic in humans. Although it is widely believed that L1s play an essential role in shaping and functioning of mammalian genomes, the understanding of the impact of L1 insertions on gene expression is far from being comprehensive. Here we compared hnRNA contents for allele pairs of genes heterozygous for Ta-L1 insertions in their introns in human cell lines of various origin. We demonstrated that some Ta-L1 insertions correlated with decreased content of the corresponding hnRNAs. This effect was characteristic of only nearly full-sized L1s and seemed to be tissue specific.
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Affiliation(s)
- Svetlana V Ustyugova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997, Moscow, Russia
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Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat 2006; 27:323-9. [PMID: 16511833 PMCID: PMC1855216 DOI: 10.1002/humu.20307] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. Since certain types of retrotransposons, particularly members of the Alu, L1, and SVA families, are still active, their recent and ongoing propagation generates a unique and important class of human genomic diversity/polymorphism (for the presence and absence of an insertion) with some elements known to cause genetic diseases. So far, over 2,300, 500, and 80 Alu, L1, and SVA insertions, respectively, have been reported to be polymorphic and many more are yet to be discovered. We present here the Database of Retrotransposon Insertion Polymorphisms (dbRIP; http://falcon.roswellpark.org:9090), a highly integrated and interactive database of human retrotransposon insertion polymorphisms (RIPs). dbRIP currently contains a nonredundant list of 1,625, 407, and 63 polymorphic Alu, L1, and SVA elements, respectively, or a total of 2,095 RIPs. In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along with all other genome annotation information. Users can query the database by a variety of means and have access to the detailed information related to a RIP, including detailed insertion sequences and genotype data. dbRIP represents the first database providing comprehensive, integrative, and interactive compilation of RIP data, and it will be a useful resource for researchers working in the area of human genetics.
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Affiliation(s)
- Jianxin Wang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
| | - Lei Song
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
| | - Deepak Grover
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, Louisiana
| | - Sami Azrak
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
| | - Mark A. Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-scale Systems, Louisiana State University, Baton Rouge, Louisiana
| | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
- * Correspondence to: Dr. Ping Liang, Department of Cancer Genetics, Roswell Park Cancer Institute, Elm & Carlton Streets, Bu¡alo, NY 14263. E-mail:
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Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E. At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. J Virol 2006; 80:10752-62. [PMID: 17041225 PMCID: PMC1641792 DOI: 10.1128/jvi.00871-06] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report the first genome-wide comparison of in vivo promoter activities of a group of human-specific endogenous retroviruses in healthy and cancerous germ line tissues. To this end, we employed a recently developed technique termed genomic repeat expression monitoring. We found that at least 50% of human-specific long terminal repeats (LTRs) possessed promoter activity, and many of them were up- or downregulated in a seminoma. Individual LTRs were expressed at markedly different levels, ranging from approximately 0.001 to approximately 3% of the housekeeping beta-actin gene transcript level. We demonstrated that the main factors affecting the LTR promoter activity were the LTR type (5'-proviral, 3' proviral, or solitary) and position with regard to genes. The averaged promoter strengths of solitary and 3'-proviral LTRs were almost identical in both tissues, whereas 5'-proviral LTRs displayed two- to fivefold higher promoter activities. The relative content of promoter-active LTRs in gene-rich regions was significantly higher than that in gene-poor loci. This content was maximal in those regions where LTRs "overlapped" readthrough transcripts. Although many promoter-active LTRs were mapped near known genes, no clear-cut correlation was observed between transcriptional activities of genes and neighboring LTRs. Our data also suggest a selective suppression of transcription for LTRs located in gene introns.
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Affiliation(s)
- Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.
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Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E. GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats. Nucleic Acids Res 2006; 34:e67. [PMID: 16698959 PMCID: PMC3303178 DOI: 10.1093/nar/gkl335] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We developed a technique called GREM (Genomic Repeat Expression Monitor) that can be applied to genome-wide isolation and quantitative analysis of any kind of transcriptionally active repetitive elements. Briefly, the technique includes three major stages: (i) generation of a transcriptome wide library of cDNA 5′ terminal fragments, (ii) selective amplification of repeat-flanking genomic loci and (iii) hybridization of the cDNA library (i) to the amplicon (ii) with subsequent selective amplification and cloning of the cDNA-genome hybrids. The sequences obtained serve as ‘tags’ for promoter active repetitive elements. The advantage of GREM is an unambiguous mapping of individual promoter active repeats at a genome-wide level. We applied GREM for genome-wide experimental identification of human-specific endogenous retroviruses and their solitary long terminal repeats (LTRs) acting in vivo as promoters. Importantly, GREM tag frequencies linearly correlated with the corresponding LTR-driven transcript levels found using RT–PCR. The GREM technique enabled us to identify 54 new functional human promoters created by retroviral LTRs.
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Affiliation(s)
- Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow 117997, Russia.
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Buzdin A, Vinogradova T, Lebedev Y, Sverdlov E. Genome-wide experimental identification and functional analysis of human specific retroelements. Cytogenet Genome Res 2005; 110:468-74. [PMID: 16093700 DOI: 10.1159/000084980] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 12/18/2003] [Indexed: 12/24/2022] Open
Abstract
Retroelements (REs) actively reshape genomes through genomic rearrangements, creation of new genes and modulation of the regulatory machinery of existing genes, thus introducing genomic novelties which potentially may be subject to natural selection. Thousands of RE integrations, presumably distinguishing the human and chimpanzee genomes, might well be involved in modern human speciation. In this self-review we describe our recent results on genome-wide identification of human specific RE integrations and their transcriptional activity obtained with three new experimental techniques (TGDA, DiffIR and SDDIR) developed by us for such studies. A new mechanism of the formation of retroelements involving template switches during L1-mediated mRNA reverse transcription, revealed in this research, will also be described in the review.
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Affiliation(s)
- A Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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21
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Ustyugova SV, Amosova AL, Lebedev YB, Sverdlov ED. Cell line fingerprinting using retroelement insertion polymorphism. Biotechniques 2005; 38:561-5. [PMID: 15884674 DOI: 10.2144/05384st02] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human cell lines are an indispensable tool for functional studies of living entities in their numerous manifestations starting with integral complex systems such as signal pathways and networks, regulation of gene ensembles, epigenetic factors, and finishing with pathological changes and impact of artificially introduced elements, such as various transgenes, on the behavior of the cell. Therefore, it is highly desirable to have reliable cell line identification techniques to make sure that the cell lines to be used in experiments are exactly what is expected. To this end, we developed a set of informative markers based on insertion polymorphism of human retroelements (REs). The set includes 47 pairs of PCR primers corresponding to introns of the human genes with dimorphic LINE1 (L1) and Alu insertions. Using locus-specific PCR assays, we have genotyped 10 human cell lines of various origins. For each of these cell lines, characteristic fingerprints were obtained. An estimated probability that two different cell lines possess the same marker genotype is about 10-18. Therefore, the proposed set of markers provides a reliable tool for cell line identification.
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Affiliation(s)
- Svetlana V Ustyugova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Han K, Sen SK, Wang J, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 2005; 33:4040-52. [PMID: 16034026 PMCID: PMC1179734 DOI: 10.1093/nar/gki718] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of approximately 18 kb of sequence from the human genome and approximately 15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.
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Affiliation(s)
| | | | - Jianxin Wang
- Department of Cancer Genetics, Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, NY 14263, USA
| | | | | | | | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, NY 14263, USA
| | - Mark A. Batzer
- To whom correspondence should be addressed. Tel: +1 225 578 7102; Fax: +1 225 578 7113;
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Gogvadze EV, Buzdin AA, Sverdlov ED. [Multiple template switches on LINE-directed reverse transcription: the most probable formation mechanism for the double and triple chimeric retroelements in mammals]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2005; 31:82-9. [PMID: 15787218 DOI: 10.1007/s11171-005-0010-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
It was shown that the shuffling mechanism for transcribed genome components, which involves a template switch on the RNA reverse transcription using the L1 retroelement enzymatic machinery, is common in mammals. The occurrence frequency of the resulting chimeric retroelements in the genomes of rodents is twice as high as in the DNA of primates. Moreover, we proved that not only single but also double switches may occur in vivo, which result in the fusion of copies of three different transcripts. Many of the identified chimeras are transcribed in mammals.
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A New Mechanism of Retrogene Formation in Mammalian Genomes: In Vivo Recombination during RNA Reverse Transcription. Mol Biol 2005. [DOI: 10.1007/s11008-005-0045-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mamedov IZ, Arzumanyan ES, Amosova AL, Lebedev YB, Sverdlov ED. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res 2005; 33:e16. [PMID: 15673711 PMCID: PMC548376 DOI: 10.1093/nar/gni018] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A new experimental technique for genome-wide detection of integration sites of polymorphic retroelements (REs) is described. The technique allows one to reveal the absence of a retroelement in an individual genome provided that this retroelement is present in at least one of several other genomes under comparison. Since quite a number of genomes are compared simultaneously, the search for polymorphic REs insertions is very efficient. The technique includes two whole-genome selective PCR amplifications of sequences flanking REs: one for a particular genome and another one for a mixture of ten different genomes. A subsequent subtractive hybridization of the obtained amplicons with DNA of a particular genome as driver results in isolation of polymorphic insertions. The technique was successfully applied for identification of 41 new polymorphic human AluYa5/Ya8 insertions. Among them, 18 individual Alu elements first sequenced in this work were not found in the available human genome databases. This result suggests that significant part of polymorphic REs were not identified during genome sequencing and remain to be detected and characterized. The proposed method does not depend on preliminary knowledge of evolutionary history of retroelements and can be applied for identification of insertion/deletion polymorphic markers in genomes of different species.
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Affiliation(s)
- Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences 16/10 Miklukho-Maklaya Street, 117997 Moscow, Russia.
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Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. The insertional history of an active family of L1 retrotransposons in humans. Genome Res 2004; 14:1221-31. [PMID: 15197167 PMCID: PMC442137 DOI: 10.1101/gr.2326704] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As humans contain a currently active L1 (LINE-1) non-LTR retrotransposon family (Ta-1), the human genome database likely provides only a partial picture of Ta-1-generated diversity. We used a non-biased method to clone Ta-1 retrotransposon-containing loci from representatives of four ethnic populations. We obtained 277 distinct Ta-1 loci and identified an additional 67 loci in the human genome database. This collection represents approximately 90% of the Ta-1 population in the individuals examined and is thus more representative of the insertional history of Ta-1 than the human genome database, which lacked approximately 40% of our cloned Ta-1 elements. As both polymorphic and fixed Ta-1 elements are as abundant in the GC-poor genomic regions as in ancestral L1 elements, the enrichment of L1 elements in GC-poor areas is likely due to insertional bias rather than selection. Although the chromosomal distribution of Ta-1 inserts is generally a function of chromosomal length and gene density, chromosome 4 significantly deviates from this pattern and has been much more hospitable to Ta-1 insertions than any other chromosome. Also, the intra-chromosomal distribution of Ta-1 elements is not uniform. Ta-1 elements tend to cluster, and the maximal gaps between Ta-1 inserts are larger than would be expected from a model of uniform random insertion.
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Affiliation(s)
- Stéphane Boissinot
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E. The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res 2003; 31:4385-90. [PMID: 12888497 PMCID: PMC169886 DOI: 10.1093/nar/gkg496] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
L1 retrotransposons play an important role in mammalian genome shaping. In particular, they can transduce their 3'-flanking regions to new genomic loci or produce pseudogenes or retrotranscripts through reverse transcription of different kinds of cellular RNAs. Recently, we found in the human genome an unusual family of chimeric retrotranscripts composed of full-sized copies of U6 small nuclear RNAs fused at their 3' termini with 5'-truncated, 3'-poly(A)-tailed L1s. The chimeras were flanked by 11-21 bp long direct repeats, and contained near their 5' ends T2A4 hexanucleotide motifs, preferably recognized by L1 nicking endonuclease. These features suggest that the chimeras were formed using the L1 integration machinery. Here we report the identification of 81 chimeras consisting of fused DNA copies of different RNAs, including mRNAs of known human genes. Based on their structural features, the chimeras were subdivided into nine distinct families. 5' Parts of the chimeras usually originated from different nuclear RNAs, whereas their 3' parts represented cytoplasmic RNAs: mRNAs, including L1 mRNA and Alu RNA. Some of these chimeric retrotranscripts are expressed in a variety of human tissues. These findings suggest that RNA-RNA recombination during L1 reverse transcription followed by the integration of the recombinants into the host genome is a general event in genome evolution.
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Affiliation(s)
- Anton Buzdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117871, Russia.
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