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Citation for Study 17406

Citation title: "Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae".

Study name: "Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae".

This study is part of submission 17406 (Status: Published).

Citation

Dai S., Hou J., Long Y., Wang J., Li C., Xiao Q., Jiang X., Zou X., Zou J., & Meng J. 2015. Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. BMC Plant Biology, .

Authors

• Dai S. (submitter) 008602787283189
• Hou J.
• Long Y.
• Wang J.
• Li C.
• Xiao Q.
• Jiang X.
• Zou X.
• Zou J.
• Meng J.

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. Conclusion: 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.

Keywords

Brassicaceae, Brassica, Miniature inverted repeat transposable elements, Monkey King, Tourist-like MITE, DNA methylation, bna-miR6031

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S17406
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24426,
  	 author = {Shutao  Dai and Jinna  Hou and Yan  Long and Jing  Wang and Cong  Li and Qinqin  Xiao and Xiaoxue  Jiang and Xiaoxiao  Zou and Jun  Zou and Jinling  meng},
  	 title = {Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae},
  	 year = {2015},
  	 keywords = {Brassicaceae, Brassica, Miniature inverted repeat transposable elements, Monkey King, Tourist-like MITE, DNA methylation, bna-miR6031},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Plant Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 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.
  Conclusion: 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.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24426
  AU  - Dai,Shutao 
  AU  - Hou,Jinna 
  AU  - Long,Yan 
  AU  - Wang,Jing 
  AU  - Li,Cong 
  AU  - Xiao,Qinqin 
  AU  - Jiang,Xiaoxue 
  AU  - Zou,Xiaoxiao 
  AU  - Zou,Jun 
  AU  - meng,Jinling 
  T1  - Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae
  PY  - 2015
  KW  - Brassicaceae
  KW  - Brassica
  KW  - Miniature inverted repeat transposable elements
  KW  - Monkey King
  KW  - Tourist-like MITE
  KW  - DNA methylation
  KW  - bna-miR6031
  UR  - http://dx.doi.org/
  N2  - 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.
  Conclusion: 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.
  
  L3  - 
  JF  - BMC Plant Biology
  VL  - 
  IS  - 
  ER  -