MAK, a Computational Tool Kit for Automated MITE Analysis

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Jun 26

PMID 12824388

Citations 28

Authors

Guojun Yang

Timothy C Hall

Affiliations

Soon will be listed here.

Abstract

Miniature inverted repeat transposable elements (MITEs) are ubiquitous and numerous in higher eukaryotic genomes. Analysis of MITE families is laborious and time consuming, especially when multiple MITE families are involved in the study. Based on the structural characteristics of MITEs and genetic principles for transposable elements (TEs), we have developed a computational tool kit named MITE analysis kit (MAK) to automate the processes (http://perl.idmb.tamu.edu/mak.htm). In addition to its ability to routinely retrieve family member sequences and to report the positions of these elements relative to the closest neighboring genes, MAK is a powerful tool for revealing anchor elements that link MITE families to known transposable element families. Implementation of the MAK is described, as are genetic principles and algorithms used in its derivation. Test runs of the programs for several MITE families yielded anchor sequences that retain TIRs and coding regions reminiscent of transposases. These anchor sequences are consistent with previously reported putative autonomous elements for these MITE families. Furthermore, analysis of two MITE families with no known links to any transposon family revealed two novel transposon families, namely Math and Kid, belonging to the IS5/Harbinger/PIF superfamily.

Citing Articles

Identification and characterization of transposable element AhMITE1 in the genomes of cultivated and two wild peanuts.

Tang Y, Li X, Hu C, Qiu X, Li J, Li X BMC Genomics. 2022; 23(1):500.

PMID: 35820800 PMC: 9277781. DOI: 10.1186/s12864-022-08732-0.

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome.

Lin L, Sharma A, Yu Q BMC Plant Biol. 2021; 21(1):424.

PMID: 34537020 PMC: 8449440. DOI: 10.1186/s12870-021-03194-0.

Identification and characterization of large-scale genomic rearrangements during wheat evolution.

Bariah I, Keidar-Friedman D, Kashkush K PLoS One. 2020; 15(4):e0231323.

PMID: 32287287 PMC: 7156093. DOI: 10.1371/journal.pone.0231323.

A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat.

Domb K, Keidar-Friedman D, Kashkush K BMC Plant Biol. 2019; 19(1):461.

PMID: 31675912 PMC: 6824096. DOI: 10.1186/s12870-019-2034-1.

Identification of an active miniature inverted-repeat transposable element mJing in rice.

Tang Y, Ma X, Zhao S, Xue W, Zheng X, Sun H Plant J. 2019; 98(4):639-653.

PMID: 30689248 PMC: 6850418. DOI: 10.1111/tpj.14260.

References

Iwamoto M, Nagashima H, Nagamine T, Higo H, Higo K . A tourist element in the 5'-flanking region of the catalase gene CatA reveals evolutionary relationships among Oryza species with various genome types. Mol Gen Genet. 1999; 262(3):493-500. DOI: 10.1007/s004380051110. View

Pereira A, Cuypers H, Gierl A, Schwarz-Sommer Z, Saedler H . Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J. 1986; 5(5):835-41. PMC: 1166871. DOI: 10.1002/j.1460-2075.1986.tb04292.x. View

Tu Z . Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc Natl Acad Sci U S A. 2001; 98(4):1699-704. PMC: 29320. DOI: 10.1073/pnas.98.4.1699. View

Charrier B, Foucher F, Kondorosi E, dAubenton-Carafa Y, Thermes C, Kondorosi A . Bigfoot. a new family of MITE elements characterized from the Medicago genus. Plant J. 1999; 18(4):431-41. DOI: 10.1111/j.1365-313x.1999.00469.x. View

Rhodes P, Vodkin L . Highly structured sequence homology between an insertion element and the gene in which it resides. Proc Natl Acad Sci U S A. 1985; 82(2):493-7. PMC: 397065. DOI: 10.1073/pnas.82.2.493. View

Nacken W, Piotrowiak R, Saedler H, Sommer H . The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specificity of insertion. Mol Gen Genet. 1991; 228(1-2):201-8. DOI: 10.1007/BF00282466. View

Braquart C, Royer V, Bouhin H . DEC: a new miniature inverted-repeat transposable element from the genome of the beetle Tenebrio molitor. Insect Mol Biol. 2000; 8(4):571-4. DOI: 10.1046/j.1365-2583.1999.00144.x. View

Oosumi T, Garlick B, Belknap W . Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1995; 92(19):8886-90. PMC: 41072. DOI: 10.1073/pnas.92.19.8886. View

Le Q, Turcotte K, Bureau T . Tc8, a Tourist-like transposon in Caenorhabditis elegans. Genetics. 2001; 158(3):1081-8. PMC: 1461737. DOI: 10.1093/genetics/158.3.1081. View

10.

Elrouby N, Bureau T . Molecular characterization of the Abp1 5'-flanking region in maize and the teosintes. Plant Physiol. 2000; 124(1):369-77. PMC: 59150. DOI: 10.1104/pp.124.1.369. View

11.

Tu Z . Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. Proc Natl Acad Sci U S A. 1997; 94(14):7475-80. PMC: 23846. DOI: 10.1073/pnas.94.14.7475. View

12.

Zhang X, Feschotte C, Zhang Q, Jiang N, Eggleston W, Wessler S . P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc Natl Acad Sci U S A. 2001; 98(22):12572-7. PMC: 60095. DOI: 10.1073/pnas.211442198. View

13.

Surzycki S, Belknap W . Characterization of repetitive DNA elements in Arabidopsis. J Mol Evol. 1999; 48(6):684-91. DOI: 10.1007/pl00006512. View

14.

Bureau T, Ronald P, Wessler S . A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci U S A. 1996; 93(16):8524-9. PMC: 38705. DOI: 10.1073/pnas.93.16.8524. View

15.

Feschotte C, Mouches C . Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo family. Gene. 2000; 250(1-2):109-16. DOI: 10.1016/s0378-1119(00)00187-6. View

16.

Surzycki S, Belknap W . Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc Natl Acad Sci U S A. 2000; 97(1):245-9. PMC: 26648. DOI: 10.1073/pnas.97.1.245. View

17.

Yang G, Dong J, Chandrasekharan M, Hall T . Kiddo, a new transposable element family closely associated with rice genes. Mol Genet Genomics. 2001; 266(3):417-24. DOI: 10.1007/s004380100530. View

18.

Bureau T, Wessler S . Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell. 1992; 4(10):1283-94. PMC: 160215. DOI: 10.1105/tpc.4.10.1283. View

19.

Tu Z, Orphanidis S . Microuli, a family of miniature subterminal inverted-repeat transposable elements (MSITEs): transposition without terminal inverted repeats. Mol Biol Evol. 2001; 18(5):893-5. DOI: 10.1093/oxfordjournals.molbev.a003871. View

20.

Bonas U, Sommer H, Saedler H . The 17-kb Tam1 element of Antirrhinum majus induces a 3-bp duplication upon integration into the chalcone synthase gene. EMBO J. 1984; 3(5):1015-9. PMC: 557465. DOI: 10.1002/j.1460-2075.1984.tb01921.x. View