Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains

Omer Baruch, Khalil Kashkush

פרסום מחקרי: פרסום בכתב עתמאמרביקורת עמיתים

תקציר

Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number.

שפה מקוריתאנגלית אמריקאית
עמודים (מ-עד)885-893
מספר עמודים9
כתב עתPlant Cell Reports
כרך31
מספר גיליון5
מזהי עצם דיגיטלי (DOIs)
סטטוס פרסוםפורסם - 1 מאי 2012

ASJC Scopus subject areas

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  • ???subjectarea.asjc.1100.1110???

טביעת אצבע

להלן מוצגים תחומי המחקר של הפרסום 'Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains'. יחד הם יוצרים טביעת אצבע ייחודית.

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