Abstract
BackgroundA transposable element (TE) is a DNA fragment that can change its position within a genome. Transposable elements play important roles in maintaining the stability and diversity of organisms by transposition. Recent studies have shown that approximately half of the genes in Bombyx mori are TEs.ResultsWe systematically identified and analyzed the BmAGO2-associated TEs, which exceed 100 in the B. mori genome. Additionally, we also mapped the small RNAs associated with BmAGO2 in B.mori. The transposon Bm1645 is the most abundant TE associated with BmAGO2, and Bm1645-derived small RNAs represent a small RNA pool. We determined the expression patterns of several Bm1645-derived small RNAs by northern blotting, and the results showed there was differential expression of multiple small RNAs in normal and BmNPV-infected BmN cells and silkworms from various developmental stages. We confirmed that four TE-siRNAs could bind to BmAGO2 using EMSA and also validated the recognition sites of these four TE-siRNAs in Bm1645 by dual-luciferase reporter assays. Furthermore, qRT-PCR analysis revealed the overexpression of the four TE-siRNAs could downregulate the expression of Bm1645 in BmN cells, and the transcription of Bm1645 was upregulated by the downregulation of BmAGO2.ConclusionsOur results suggest Bm1645 functions as a source of small RNAs pool and this pool can produce many BmAGO2-associated small RNAs that regulate TE’s expression.
Highlights
A transposable element (TE) is a DNA fragment that can change its position within a genome
Sequencing and analysis of BmAGO2-associated TEs and BmAGO2-associated small RNAs In our previous work, we confirmed that BmAGO2 could associate with TE-small interfering RNAs (siRNAs) derived from several TEs [26]
To determine if BmAGO2 could associate with TEs, we successfully isolated the BmAGO2-associated RNAs from BmN cells by immunoprecipitation (IP) according to the previous method [26] (Additional file 1: Figure S1) and the >200 nt fraction was size-fractionated for deep sequencing (LC Sciences)
Summary
A transposable element (TE) is a DNA fragment that can change its position within a genome. Recent studies have shown that approximately half of the genes in Bombyx mori are TEs. Results: We systematically identified and analyzed the BmAGO2-associated TEs, which exceed 100 in the B. mori genome. The transposon Bm1645 is the most abundant TE associated with BmAGO2, and Bm1645-derived small RNAs represent a small RNA pool. The Argonaute (AGO) protein family contains proteins that are highly conserved throughout evolution. These proteins are the core components of the RNA-induced silencing complex (RISC) that function to silence gene expression in both plants and animals [1,2,3,4]. There were four members of the AGO family systemically identified in Bombyx mori [5]. The first two members belong to the AGO subfamily, and the latter two proteins are members of the PIWI subfamily
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