title: Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae.
abstract: BACKGROUND
  Miniature inverted repeat transposable elements (MITEs) are important components of eukaryotic genomes, with hundreds of families and many copies, which may play important roles in gene regulation and genome evolution. However, few studies have investigated the molecular mechanisms involved. In our previous study, a Tourist-like MITE, Monkey King, was identified from the promoter region of a flowering time gene, BnFLC.A10, in Brassica napus. Based on this MITE, the characteristics and potential roles on gene regulation of the MITE family were analyzed in Brassicaceae.
  
  
  RESULTS
  The characteristics of the Tourist-like MITE family Monkey King in Brassicaceae, including its distribution, copies and insertion sites in the genomes of major Brassicaceae species were analyzed in this study. Monkey King was actively amplified in Brassica after divergence from Arabidopsis, which was indicated by the prompt increase in copy number and by phylogenetic analysis. The genomic variations caused by Monkey King insertions, both intra- and inter-species in Brassica, were traced by PCR amplification. Genomic sequence analysis showed that most complete Monkey King elements are located in gene-rich regions, less than 3kb from genes, in both the B. rapa and A. thaliana genomes. Sixty-seven Brassica expressed sequence tags carrying Monkey King fragments were also identified from the NCBI database. Bisulfite sequencing identified specific DNA methylation of cytosine residues in the Monkey King sequence. A fragment containing putative TATA-box motifs in the MITE sequence could bind with nuclear protein(s) extracted from leaves of B. napus plants. A Monkey King-related microRNA, bna-miR6031, was identified in the microRNA database. In transgenic A. thaliana, when the Monkey King element was inserted upstream of 35S promoter, the promoter activity was weakened.
  
  
  CONCLUSIONS
  Monkey King, a Brassicaceae Tourist-like MITE family, has amplified relatively recently and has induced intra- and inter-species genomic variations in Brassica. Monkey King elements are most abundant in the vicinity of genes and may have a substantial effect on genome-wide gene regulation in Brassicaceae. Monkey King insertions potentially regulate gene expression and genome evolution through epigenetic modification and new regulatory motif production.
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. daishutao@webmail.hzau.edu.cn.
authors.forename: Shutao
authors.initials: S
authors.lastname: Dai
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. houjinna@hnagri.org.cn.|Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhenzhou, Henan, 450002, China. houjinna@hnagri.org.cn.
authors.forename: Jinna
authors.initials: J
authors.lastname: Hou
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. longyan@caas.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Long
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. wangjing@mail.hzau.edu.cn.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. lic@webmail.hzau.edu.cn.
authors.forename: Cong
authors.initials: C
authors.lastname: Li
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. xiaoqq027@163.com.
authors.forename: Qinqin
authors.initials: Q
authors.lastname: Xiao
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. xue19870214@gmail.com.
authors.forename: Xiaoxue
authors.initials: X
authors.lastname: Jiang
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. zxxyp@webmail.hzau.edu.cn.
authors.forename: Xiaoxiao
authors.initials: X
authors.lastname: Zou
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. zoujun@mail.hzau.edu.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Zou
authors.affiliation: National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. jmeng@mail.hzau.edu.cn.
authors.forename: Jinling
authors.initials: J
authors.lastname: Meng
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D019607:Brassicaceae / Q000235:genetics*; D002874:Chromosome Mapping; D003198:Computer Simulation; D019175:DNA Methylation / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay; D019143:Evolution, Molecular; D018745:Genome, Plant; D055029:Inverted Repeat Sequences / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000235:genetics; D009687:Nuclear Proteins / Q000378:metabolism; D010802:Phylogeny; D030821:Plants, Genetically Modified; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D009687:Nuclear Proteins