Transposons Continue the Amaze

Yıl 2019, , 1 - 13, 19.08.2019

Nermin Gozukirmizi

https://doi.org/10.38058/ijsl.585052

Cited By: 2

Öz

Transposable
elements (TEs)
were first discovered in maize plants. However, they
exist almost in all species with a few exceptions (Plasmodium falciparum,
Ashbya gossypii and Kluveromuyces lactis). They are the most important contributors to genome
plasticity and evolution and even epigenetic genome regulation. Organisms
with large genomes have high transposon percentages. For example, Arabidopsis
thaliana has a genome size of 125 Mb which comprises 14% transposons, Homo sapiens (3000 Mb) 45-48.5%, and Hordeum
vulgare genome (5300 Mb) has 80%. TEs are classified into two major groups
based on their transposition mechanisms: Class I (RNA transposons –
retrotransposons) and Class II (DNA transposons). Recent progress in whole-genome sequencing and long-read
assembly have resulted in identification of unprecedentedly long transposable
units spanning dozens or even hundreds of kilobases, initially in prokaryotic
and more recently in eukaryotic systems. All TEs in a cell are
named as transposome (mobilome), and transposomics is a new area to work with
transposome. Although a number of bioinformatics softwares have recently been
developed for the annotation of TEs in sequenced genomes, there are very few
computational tools strictly dedicated to the identification of active TEs
using genome-wide approaches. In this review article, after a brief
introduction and review of the transposable elements, I discussed their effects
in gene expression, evolution, recent applications and also share our research on
retrotransposons with different organisms.

Anahtar Kelimeler

Evolution, Genome dynamics, Mobile elements, Over-sized transposable elements, , Transposon based genome editing

Teşekkür

I would like to give my sincere thanks to young researchers (Msc and PhD students) whose together with me during transposon studies. I also would like to thank Istanbul University Molecular Biology Genetics Department, Istanbul University Research Fund supporting us during our transposon research.

Kaynakça

• Agarwal, M., Shrivastava, N., Padh, H. 2008. Advances in molecular marker techniques and their applications in plant sciences, Plant Cell Reports, 27: 617-631.Amselem, J., Cornut G., Choisne N., Alaux M., Alfama-Depauw F., Jamilloux, V., Maumus, F., Letellier, T., Luyten, I., Pommier, C., Adam-Blondon, A.F., Quesneville, H. 2019. RepetDB: a unified resource for transposable element references, Mobile DNA, 10:6:1-8.Arkhipova, I.R., Yushenova, I.A., 2019, Giant transposons in eukaryotes: Is bigger better?, Genome Biology and Evolution, 11: 906-918. Bayram, E., Yilmaz, S., Hamat-Mecbur, H., Kartal-Alacam, G. 2012. Nikita retrotransposon movements in callus cultures of barley (Hordeum vulgare L.), Plant Omics, 5: 211-215.Bennetzen, J.L. 2005. Transposable elements, gene creation and genome rearrangement in flowering plants, Current Opinion in Genetics & Development, 15: 621-627.Boissinot, S., Bourgeois, Y., Manthey, J.D., Ruggiero, R.P. 2019. The mobilome of reptiles: evolution, structure, and function, Cytogenetic and Genome Research, 157: 21-33.Buckley, R.M., Adelson, D.L. 2014. Mammalian genome evolution as a result of epigenetic regulation of transposable elements, Biomol Concepts, 5: 183–94.Cakmak, B., Marakli, S., Gozukirmizi, N. 2015. SIRE1 retrotransposons in barley (Hordeum vulgare L.), Russian Journal of Genetics, 51: 661-662. Cakmak, B., Marakli, S., Gozukirmizi, N. 2017. Sukkula retrotransposon movements in the human genome, Biotechnology & Biotechnological Equipment, 31: 756- 760. Cakmak, B., Gozukirmizi, N. 2018. Origin and distribution of different retrotransposons in different taxa, Genetics & Applications, 2: 13-19.Cho, J. 2018. Transposon-derived non-coding RNAs and their function in plants. Frontiers in Plant Science, 9: 600. Deniz, O., Frost, J. M., Branco M. R. 2019. Regulation of transposable elements by DNA modifications. Nature Reviews Genetics, 20: 417-431. Dupeyron, M., Singh, K. S., Bass, C., Hayward, A. 2019. Evolution of mutator transposable elements across eukaryotic diversity. Mobile DNA, 10: 12.Ellinghaus, D.1., Kurtz, S., Willhoeft, U. 2008. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9: 18.Evrensel, C., Yilmaz, S., Temel, A., Gozukirmizi, N. 2011. Variations in BARE-1 insertion patterns in barley callus cultures, Genetics and Molecular Research, 10: 980-987.Feschotte, C., Jiang, N., Wessler, S.R. 2002. Plant transposable elements: where genetics meets genomics, Nature Reviews Genetics, 3: 329-341.Gozukirmizi, N., Yilmaz, S., Marakli, S., Temel, A. 2015. Retrotransposon-based molecular markers; tools for variation analysis in plants. In: Tashki, K., Pandalai, S. (Eds). Applications of Molecular Markers in Plant Genome Analysis and Breeding. Research Signpost/Transworld Research Network Kerala, India. pp. 19-45. Gozukirmizi, N., Temel, A., Marakli, S., Yilmaz, S. 2016. Transposon activity in plant genomes. In: Hakeem, K.R., Tombuloglu, H., Tombuloğlu, G. (Eds). Plant Omics Trends and Applications. Springer International Publishing Switzerland. pp. 83-108. Hall, A.E., Kettler, G.C., Preuss, D. 2006. Dynamic evolution at pericentromeres, Genome Research, 16: 355-364. Hamat-Mecbur, H., Yilmaz, S., Temel, A., Sahin, K., Gozukirmizi, N. 2014. Effects of epirubicin on barley seedlings, Toxicology and Industrial Health, 30: 52-59.https://www.earthbiogenome.org, June 2019.http://botserv2.uzh.ch/kelldata/trep-db/index.html, June 2019.Joly-Lopez, Z., Bureau, T.E. 2014. Diversity and evolution of transposable elements in Arabidopsis, Chromosome Research, 22: 203-216.Kalendar, R., Schulman, A.H., 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting, Nature Protocols, 1: 2478-2484.Kapitonov, V.V., Jurka, J. 2008. A universal classification of eukaryotic transposable elements implemented in Repbase, Nature Reviews Genetics, 9: 411-412.Kapusta, A., Suh, A., Feschotte, C. 2017. Dynamics of genome size evolution in birds and mammals, Proceedings of the National Academy of Sciences of the United States of America, 114: 1460–1469.Karlik, E., Albayrak, M., Uzen, E., Gozukirmizi N. 2019. Transposon studies on Colchium chalcedonicum, International Journal of Life Sciences and Biotechnology, 2: 25-35.Kartal, G., Yilmaz, S., Marakli, S., Gozukirmizi, N. 2014. Sukkula retrotransposon insertion polymorphism in barley. Russian Journal of Plant Physiology, 61: 828-833.Kaya, Y., Yilmaz, S., Gozukirmizi, N., Huyop, F. 2013. Evaluation of transgenic Nicotiana tabacum with dehE gene using transposon based IRAP markers, American Journal of Plant Sciences, 4: 41-44.Kazazian, H.H. 2004. Mobile elements: drivers of genome evolution, Science, 303:1626-1632.Klompe, S.E., Vo, P.L.H., Halpin-Healy, T.S., Sternberg, S.H. 2019. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration, Nature, doi:10.1038/s41586-019-1323-z.Lerat, E., Casacuberta, J., Chaparro, C., Vieira, C. 2019. On the importance to acknowledge transposable elements in epigenomic analyses, Genes, 10, 258. Ma, J., Wing, R.A., Bennetzen, J.L., Jackson, S.A. 2007. Plant centromere organization: a dynamic structure with conserved functions, Trends in Genetics, 23: 134-139. Madlung, A., Comai, L. 2004. The effect of stress on genome regulation and structure. Annals of Botany, 94: 481-495. Marakli, S., Yilmaz, S., Gozukirmizi, N. 2012. BARE1 and BAGY2 retrotransposon movements and expression analyses in developing barley seedlings, Biotechnology & Biotechnological Equipment, 26: 3451-3456.Marakli, S., Calis, A., Gozukirmizi, N., 2019. Determination of barley-specific retrotransposons’ movements in Pinus nigra ssp. pallasiana varieties: pyramidata and Seneriana, Russian Journal of Genetics, 55: 71-78.McClintock, B. 1950. The origin and behavior of mutable loci in maize, Proceedings of the National Academy of Sciences of the United States of America, 36: 34-355.Morgante, M., De Paoli, E., Radovic, S. 2007. Transposable elements and the plant pan-genomes, Current Opinion in Plant Biology, 10: 149-155.Piégua, B., Birea, S., Arensburgera P., Bigot Y. 2015. A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity. Molecular Phylogenetics and Evolution, 86: 90-109.Poczai, P., Varga, I., Laos, M., Cseh, A., Bell, N., Valkonen, J.PT, Hyvonen, J. 2013. Advances in plant gene-targeted and functional markers: a review. Plant Methods, 9: 6.Poulter, R.T., Goodwin, T.J. 2005. DIRS-1 and the other tyrosine recombinase retrotransposons, Cytogenetic and Genome Research, 110: 575-588.Reiss, D., Mialdea, G., Miele, V, de Vienne, D.M., Peccoud, J., Gilbert, C., Duret, L., Charlat, S. 2019. Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot, PLoS Genetics, 15: e1007965. Slotkin, R.K., Nuthikattu, S., Jiang, N. 2012. The impact of transposable elements on gene and genome evolution. In: Wendel, J.F., Greilhuber, J., Dolezel, J., Leitch, I.J. (Eds). Plant Genome Diversity. Springer Vienna. pp. 35-58.Schrader, L., Schmitz, J. 2019. The impact of transposable elements in adaptive evolution, Molecular Ecology, 28: 1537-1549.Szabo, M., Kiss, J., Olasz, F. 2010. Functional organization of the inverted repeats of IS30. Journal of Bacteriology, 192: 3414-3423.Temel, A., Gozukirmizi, N. 2013. Analysis of retrotransposition and DNA methylation in barley callus culture, Acta Biologica Hungarica, 64: 86-95. Temel, A., Gozukirmizi, N. 2014. Genotoxicity of metaphase-arresting methods in barley, Turkish Journal of Biology, 39: 39-46.The Arabidopsis Genome Initiative 2000The International Brachypodium Initiative 2010Weil, C., Martienssen, R. 2008. Epigenetic interactions between transposons and genes: lessons from plants, Current Opinion in Genetics & Development, 18: 188-192.Yilmaz, S., Gozukirmizi, N. 2013. Variation of retrotransposon movement in callus culture and regenerated shoots of barley, Biotechnology & Biotechnological Equipment, 27: 4227-4230.Yilmaz, S., Marakli, S., Gozukirmizi, N. 2014. BAGY2 retrotransposon analyses in barley calli cultures and regenerated plantlets, Biochemical Genetics, 52: 233-244.Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., Schulman, A.H. 2007. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8: 973-982.Valencia, J. D., Girgis H. Z. 2019. LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo, BMC Genomics, 20: 450.Xu, Z., Wang H. 2008. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Research, W265–W268. Yilmaz S., Marakli S., Yuzbasioglu G., Gozukirmizi N. 2018. Short-term mutagenicity test by using IRAP molecular marker in rice grown under herbicide treatment, Biotechnology & Biotechnological Equipment, 32: 923-928.Yuzbasioglu, G., Yilmaz, S., Marakli, S., Gozukirmizi, N. 2016a. Analysis of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice, Biotechnology & Biotechnological Equipment, 30: 213-218. Yüzbaşıoğlu, G., Yilmaz, S., Gozukirmizi, N. 2016b. Houba retrotransposon based molecular markers a tool for variation analysis in rice, Turkish Journal of Agriculture and Forestry, 40: 456-464. Zeng L., Pederson S.M., Kortschak R.D., David L. 2018. Transposable elements and gene expression during the evolution of amniotes, Mobile DNA, 9: 17.