Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome
Abstract
:1. Introduction
2. Transposons as a Source of Repetitive Units for the Emergence of Tandem Repeats
2.1. Classes and Mobility of the TEs
2.2. Are Certain Portions of a TE More Prone to the Generation of Tandem Repeat Sequences?
3. Is the Centromeric Region a Hotspot of the Emergence of de novo satDNA Derived from TEs?
4. Mechanisms of the Production of Repeats from TEs
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Type of Transposable Element (TE) | Superfamily | Class | Mobility | Region of the TE | New Sequence | Reference |
---|---|---|---|---|---|---|---|
Pan paniscus and Hylobates lar | Alu elements | SINE Alu Family | Class I | non-autonomous | 3′ oligo(dA) tail and A-rich middle region | A-rich primates’ microsatellites | [69] |
Homo sapiens | Alu | LTR –retrotransposons | SINE Alu Family | Class I | non-autonomous | TR may occur in any region of the TE | 7276 Minisatellites | [61] |
Homo sapiens | Alu | SINE Alu Family | Class I | non-autonomous | - | pλg3, pMSl, pMS43, and pMS228 | [66] |
Homo sapiens | Alu | SINE Alu Family | Class I | non-autonomous | Near to 3′ -UTR. | Three minisatellites | [68] |
Homo sapiens | Alu | SINE Alu Family | Class I | non-autonomous | 3′ oligo(dA) tail. | (GAA)n | [67] |
Mouse genome | SINE B1 | SINE Superfamily | Class I | non-autonomous | GAGGCA dimmer within the SINE | (GGCAGA)n | [78] |
Mouse genome | MaLR | Retrotransposon-like superfamily | Class I | non-autonomous | LTR | Ms6-hm e Hm-2 | [79] |
Ctenomys sp. | retroviral genome | - | Class I | - | LTR | RPCS satDNA | [80] |
Phodopus roborovskii | LINE-1 elements | LINE | Class I | autonomous | ORF2 | PROsat | [81] |
Dolphin | LINE-1 | LINE | Class I | autonomous | -3’ UTR | Common Cetacean Satellite | [82] |
Phoca vitulina concolour | LINE-1 | LINE | Class I | autonomous | ORF2 | Pvc 20 | [83] |
Genus Messor | Mariner-like (Mboumar) | Tc1/mariner | Class II | autonomous | Mariner is found inside the satDNA | satDNA | [84] |
Gallus gallus | CR1 | CR1 family of LINEs | Class I | autonomous | -3′ UTR and a partial coding region of ORF 2 | HinfI (SCR1) | [7] |
Helicoverpa zea | HzSINE1 MITE-like | SINE Superfamily | Class II | non-autonomous | 5′-IR | (GTCY)n | [72] |
Drosophila virilis, Drosophila americana, and Drosophila biarmipes. | DINEs | Helitron | Class II | non-autonomous | Central tandem repeats (CTRs) | satDNA arrays | [8] |
Drosophila guanche | SGM-IS | SGM Transposon Family | Class II | non-autonomous | - | SGM satDNA | [85] |
Drosophila virilis group | pDv element | pDv transposable element family | Class II | - | Terminal repeat | pvB370 BamHI sat DNA | [86] |
Drosophila melanogaster | TART | HeT-A | TART subfamilies of the HeT DNA family | Class I Class I | Autonomous non-autonomous | -3’ UTR | 18HT satDNA | [87] |
Drosophila virilis | Tetris | Foldback elements | Class II | non-autonomous | TIR | satDNA-arrays (TIR-220) | [88] |
Hydromantes imperialis and H. ambrosii | SINE-like elements | SINE Superfamily | Class I | non-autonomous | tRNA-related region | Hy/Pol III | [89] |
Monopterus albus | LTR- RetrotransposonGypsy | LTR-Retrotransposon-like | Class I | autonomous | LTR | satDNA MALREP | [90] |
Xenopus leavis | Xmix MITE | - | Class II | non-autonomous | TIR | Xstir satDNA | [73] |
Xenopus leavis | SINE-like | SINE Superfamily | Class I | non-autonomous | tRNA-related region | Satellite 1 | [91] |
Xenopus tropicalis | MITE of TC1-mariner | Tc1–Mariner | Class II | non-autonomous | stDNA located within the MITE element | miDNA4 | [74] |
Ostrea edulis | CvA | Pearl | Class II | non-autonomous | - | HindIII | [77] |
Venerupis decussata | MITE (Pearl) | Pearl | Class II | non-autonomous | - | BIV160 | [92] |
Arabidopsis thaliana | Atenspm | En/Spm-like | Class II | autonomous | -5’ UTR | ENSAT1 | [93] |
Pisum sativum | Ty3/gypsy-like ogre | Gypsy | Class I | autonomous | -3′ UTR | PisTR-A satDNA | [59] |
Glycine max | Gmr9/GmOgre | Ty3-gypsy | Class I | autonomous | Between the 3’UTR and Repetitive LTR | Gmr9-associate minisatellite | [94] |
Solanum bulbocastanum | Sore 1 | SORE-1 family | Class I | autonomous | LTR | Sobo satDNa | [6] |
Solanum tuberosus | Ty3/gypsy-like | LTR-Retrotransposon-like | Class I | autonomous | LTR | St3-58; St3-238; St18; St3-294 | [95] |
Zea mays | CRM1 and CRM4 | Centromeric Retrotransposons of Maize (CRM) | Class I | autonomous | UTR regions and LTR | CRM1TR e CRM4TR satDNA | [96] |
Hordeum vulgare | BARE-1 | BARE-1 retrotransposon family | Class I | non-autonomous | LTR | SSR | [97] |
Aegilops speltoides | Cereba | Ty3-gypsy | Class I | autonomous | ORF to gag | CAA microsatellite | [98] |
Secale cereale | Crwydryn Tnr1 MITE | Crwydryn Tnr1/Stowaway family | Class I Class II | non-autonomous non-autonomous | ORF to gag - | E3900 satDNA D1100 satDNA | [75] |
Lathyrus sativus | Ogre LTR-retrotransposons | LTR-Retrotransposon-like | Class I | autonomous | Close to the ORF to gag | nine satDNAs. | [99] |
Chenopodium album aggregate | CACTA-Like Jozin | CACTA superfamily | Class II | non-autonomous | Tnp2 TPase | CficCl-61-40 satDNA | [4] |
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Zattera, M.L.; Bruschi, D.P. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022, 11, 3373. https://doi.org/10.3390/cells11213373
Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells. 2022; 11(21):3373. https://doi.org/10.3390/cells11213373
Chicago/Turabian StyleZattera, Michelle Louise, and Daniel Pacheco Bruschi. 2022. "Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome" Cells 11, no. 21: 3373. https://doi.org/10.3390/cells11213373
APA StyleZattera, M. L., & Bruschi, D. P. (2022). Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells, 11(21), 3373. https://doi.org/10.3390/cells11213373