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Miniature Inverted-repeat Transposable Elements

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Miniature Inverted-repeat Transposable Elements (MITEs) are a group of non-autonomous Class II transposable elements (DNA sequences). Being non-autonomous, MITEs cannot code for their own transposase. They exist within the genomes of animals, plants, fungi, bacteria and even viruses.[1][2][3][4][5][6] MITEs are generally short (50 to 500 bp) elements with terminal inverted repeats (TIRs; 10–15 bp) and two flanking target site duplications (TSDs). Like other transposons, MITEs are inserted predominantly in gene-rich regions and this can be a reason that they affect gene expression and play important roles in accelerating eukaryotic evolution.[7][8] Their high copy number in spite of small sizes has been a topic of interest.

Origin of MITEs

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A detailed study of MITEs reveals that MITE subfamilies have arisen from related autonomous elements from a single genome and these subfamilies constitute the MITE families. One type of autonomous element can give rise to one or more MITE families.[9]

Classification

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Based on their relations in sequences of TIRs with known TE superfamilies, MITEs have been classified into certain families. For example, wTourist, Acrobat, Hearthealer are MITE families in some plant species are under the TE superfamily PIF/Harbinger. Stowaway is a MITE family in Pisum sativum L. with TSD TA in relation to Tc1/mariner TE superfamily. A group of MITEs known as CMITES related to Piggybac superfamily were found in certain coral species.[10]

While most of the MITEs are grouped, some of them are yet to be allotted their TE superfamilies. Such families include AtATE in Arabidopsis thaliana and ATon family found in Aedes aegypti. Besides this, many more MITE families are likely to be discovered.

MITEs in Plant Genomes

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MITEs were first discovered in plants. Elements belonging to the CACTA, hAT, Mutator, PIF, and Tc1/Mariner superfamilies have been described.[11] Depending upon the similarity of their terminal inverted repeats and target site duplications, most of the MITEs in plant genomes are divided into two major groups: Tourist-like MITEs (derived from PIF)[12] and Stowaway-like MITEs (derived from Tc1/mariner).[13]Stowaway and Tourist elements differ remarkably in their sequences. Still, they have been found to have significant structural similarities.

Stowaway elements possess target site specificity, have small size and conserved terminal inverted repeat. So is the case determined in Tourist like MITEs. They can form stable DNA secondary structures which can be very useful in identifying them. A few Stowaway elements also contain cis-acting regulatory domains.

Other MITE superfamilies have also been described in plants, such as hAT-type MITEs in banana[14] and the nightshades.[15]

MITEs as Genetic Markers

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Based on the presence or absence of MITE family Heartbreaker (Hbr) in maize genome, a molecular marker was developed. These Hbr markers have been proved to be stable, uniformly distributed in maize genome. A study by Casa et al. showed that HBr markers could be used along with other molecular markers to study genotype of related maize inbred lines.[16]

Computational Assistance

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Software like FINDMITE use sequence entries of some average sized bp to identify MITE families. A MATLAB-based program called detectMITE can detect MITEs on a genome wide scale and was tested on the rice genome.[17] Other tools like MUST and MITE-Hunter are also used for similar purposes. To characterize MITE families a toolkit has been developed called MITE Analysis Kit MAK by Yang and Hall.[18]

References

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  1. ^ Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H (March 2012). "Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa". Molecular Biology and Evolution. 29 (3): 1005–17. doi:10.1093/molbev/msr282. PMC 3278479. PMID 22096216.
  2. ^ Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S (May 2012). "Characterization of active miniature inverted-repeat transposable elements in the peanut genome". Theoretical and Applied Genetics. 124 (8): 1429–38. doi:10.1007/s00122-012-1798-6. PMC 3336055. PMID 22294450.
  3. ^ Siguier P, Filée J, Chandler M (October 2006). "Insertion sequences in prokaryotic genomes". Current Opinion in Microbiology. 9 (5): 526–31. doi:10.1016/j.mib.2006.08.005. PMID 16935554.
  4. ^ Bardaji L, Añorga M, Jackson RW, Martínez-Bilbao A, Yanguas-Casás N, Murillo J (2011). "Miniature transposable sequences are frequently mobilized in the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola". PLOS ONE. 6 (10): e25773. Bibcode:2011PLoSO...625773B. doi:10.1371/journal.pone.0025773. PMC 3189936. PMID 22016774.
  5. ^ Sun, Cheng; Feschotte, Cédric; Wu, Zhiqiang; Mueller, Rachel Lockridge (12 June 2015). "DNA transposons have colonized the genome of the giant virus Pandoravirus salinus". BMC Biology. 13: 38. doi:10.1186/s12915-015-0145-1. PMC 4495683. PMID 26067596.
  6. ^ Zhang, Hua-Hao; Zhou, Qiu-Zhong; Wang, Ping-Lan; Xiong, Xiao-Min; Luchetti, Andrea; Raoult, Didier; Levasseur, Anthony; Santini, Sebastien; Abergel, Chantal; Legendre, Matthieu; Drezen, Jean-Michel; Béliveau, Catherine; Cusson, Michel; Jiang, Shen-Hua; Bao, Hai-Ou; Sun, Cheng; Bureau, Thomas E.; Cheng, Peng-Fei; Han, Min-Jin; Zhang, Ze; Zhang, Xiao-Gu; Dai, Fang-Yin (2018). "Unexpected invasion of miniature inverted-repeat transposable elements in viral genomes". Mobile DNA. 9: 19. doi:10.1186/s13100-018-0125-4. PMC 6004678. PMID 29946369. {{cite journal}}: |last17= has generic name (help)
  7. ^ Zhang, Q.; Arbuckle, J.; Wessler, S. R. (2000). "Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize". Proceedings of the National Academy of Sciences. 97 (3): 1160–1165. Bibcode:2000PNAS...97.1160Z. doi:10.1073/pnas.97.3.1160. PMC 15555. PMID 10655501.
  8. ^ Feschotte C, Jiang N, Wessler SR (May 2002). "Plant transposable elements: where genetics meets genomics". Nature Reviews. Genetics. 3 (5): 329–41. doi:10.1038/nrg793. PMID 11988759. S2CID 32630879.
  9. ^ Feschotte C, Zhang X, Wessler SR (2002). "Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons". In Craig N, Craigie R, Gellert M, Lambowitz A (eds.). Mobile DNA II (2nd ed.). Washington, D.C.: American Society of Microbiology Press. pp. 1147–1158. ISBN 978-1-55581-209-6.
  10. ^ Wang S, Zhang L, Meyer E, Matz MV (May 2010). "Characterization of a group of MITEs with unusual features from two coral genomes". PLOS ONE. 5 (5): e10700. Bibcode:2010PLoSO...510700W. doi:10.1371/journal.pone.0010700. PMC 2872659. PMID 20502527.
  11. ^ Feschotte C, Pritham EJ (2007). "DNA transposons and the evolution of eukaryotic genomes". Annual Review of Genetics. 41: 331–68. doi:10.1146/annurev.genet.40.110405.090448. PMC 2167627. PMID 18076328.
  12. ^ Zhang X, Jiang N, Feschotte C, Wessler SR (February 2004). "PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements". Genetics. 166 (2): 971–86. doi:10.1534/genetics.166.2.971. PMC 1470744. PMID 15020481.
  13. ^ Bureau TE, Wessler SR (June 1994). "Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants". The Plant Cell. 6 (6): 907–16. doi:10.2307/3869968. JSTOR 3869968. PMC 160488. PMID 8061524.
  14. ^ Menzel G, Heitkam T, Seibt KM, Nouroz F, Müller-Stoermer M, Heslop-Harrison JS, Schmidt T (December 2014). "The diversification and activity of hAT transposons in Musa genomes". Chromosome Research. 22 (4): 559–71. doi:10.1007/s10577-014-9445-5. PMID 25377178. S2CID 15642479.
  15. ^ Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B (January 2009). "Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs". Genome Research. 19 (1): 42–56. doi:10.1101/gr.078196.108. PMC 2612961. PMID 19037014.
  16. ^ Casa AM, Mitchell SE, Smith OS, Register JC, Wessler SR, Kresovich S (January 2002). "Evaluation of Hbr (MITE) markers for assessment of genetic relationships among maize ( Zea mays L.) inbred lines". Theoretical and Applied Genetics. 104 (1): 104–10. doi:10.1007/s001220200012. PMID 12579434. S2CID 23328113.
  17. ^ Ye C, Ji G, Liang C (January 2016). "detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes". Scientific Reports. 6 (1): 19688. Bibcode:2016NatSR...619688Y. doi:10.1038/srep19688. PMC 4726161. PMID 26795595.
  18. ^ Yang, Guojun; Hall, Timothy C. (2003-07-01). "MAK, a computational tool kit for automated MITE analysis". Nucleic Acids Research. 31 (13): 3659–3665. doi:10.1093/nar/gkg531. ISSN 0305-1048. PMC 168938. PMID 12824388.
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