Bombyx small RNAs: Genomic defense system against transposons in the silkworm, Bombyx mori

Kawaoka, Shinpei; Hayashi, Nobuko; Katsuma, Susumu; Kishino, Hirohisa; Kohara, Yuji; Mita, Kazuei; Shimada, Toru

doi:10.1016/j.ibmb.2008.03.007

Cited by 41 publications

(49 citation statements)

References 59 publications

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“…We observed differences in small RNA profiles derived from BmN4 cells and Bombyx ovary. In the case of SART1, ovary-derived small RNAs were mapped almost exclusively to ORF2 (Kawaoka et al 2008b), while this feature was not observed in BmN4-derived small RNAs (Supplemental Fig. 1).…”

Section: Identification and Characterization Of Pirnas In Bmn4 Cellsmentioning

confidence: 96%

“…Based on our previous observations of a huge amount of piRNAs in the silkworm Bombyx mori ovary (Kawaoka et al 2008b), we sought for piRNA-like small RNA-expressing cell lines derived from ovaries of several lepidopteran insect species to establish an in vitro experimental system for piRNA research. As shown in Figure 1A, we found that a distinct population of small RNAs around 27-28 nucleotides (nt) long are expressed in Bombyx-derived BmN4, Trichoplusia ni-derived High Five, and Spodoptera frugiperda-derived Sf9 cells.…”

Section: Identification and Characterization Of Pirnas In Bmn4 Cellsmentioning

confidence: 99%

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The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

Kawaoka¹,

Hayashi²,

Suzuki³

et al. 2009

RNA

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128

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Genetic studies and large-scale sequencing experiments have revealed that the PIWI subfamily proteins and PIWI-interacting RNAs (piRNAs) play an important role in germ line development and transposon control. Biochemical studies in vitro have greatly contributed to the understanding of small interfering RNA (siRNA) and microRNA (miRNA) pathways. However, in vitro analyses of the piRNA pathway have been thus far quite challenging, because their expression is largely restricted to the germ line. Here we report that Bombyx mori ovary-derived cultured cell line, BmN4, endogenously expresses two PIWI subfamily proteins, silkworm Piwi (Siwi) and Ago3 (BmAgo3), and piRNAs associated with them. Siwi-bound piRNAs have a strong bias for uridine at their 59 end and BmAgo3-bound piRNAs are enriched for adenine at position 10. In addition, Siwi preferentially binds antisense piRNAs, whereas BmAgo3 binds sense piRNAs. Moreover, we identified many pairs in which Siwi-bound antisense and BmAgo3-bound sense piRNAs are overlapped by precisely 10 nt at their 59 ends. These signatures are known to be important for secondary piRNA biogenesis in other organisms. Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function.

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Section: Identification and Characterization Of Pirnas In Bmn4 Cellsmentioning

confidence: 96%

Section: Identification and Characterization Of Pirnas In Bmn4 Cellsmentioning

confidence: 99%

The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

Kawaoka¹,

Hayashi²,

Suzuki³

et al. 2009

RNA

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128

192

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“…Analysis of HDV-like ribozymes in mosquitoes showed that both expression levels and the cleavage extent vary through the developmental stages of Genomic hammerhead ribozymes www.rnajournal.org 879 the insect, suggesting that the ribozyme self-scission is indeed regulated (Webb et al 2009). A potential mechanism of ribozyme regulation may involve short antisense RNAs, such as those found to map to a putative HDV-like ribozyme in silkworm retrotransposons (Kawaoka et al 2008;Ruminski et al 2011).…”

Section: Stem I-ii Tertiary Interaction and Unusual Variantsmentioning

confidence: 99%

The ubiquitous hammerhead ribozyme

Hammann¹,

Lupták²,

Perreault³

et al. 2012

RNA

124

116

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The hammerhead ribozyme is a small catalytic RNA motif capable of endonucleolytic (self-) cleavage. It is composed of a catalytic core of conserved nucleotides flanked by three helices, two of which form essential tertiary interactions for fast selfscission under physiological conditions. Originally discovered in subviral plant pathogens, its presence in several eukaryotic genomes has been reported since. More recently, this catalytic RNA motif has been shown to reside in a large number of genomes. We review the different approaches in discovering these new hammerhead ribozyme sequences and discuss possible biological functions of the genomic motifs.

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“…Chimeric piRNAs were not found in the WT BmN4-derived library. Density of piRNAs was normalized as described previously (Brennecke et al 2007;Kawaoka et al 2008b). See also Supplemental Figure S5.…”

Section: Establishment Of Multiple Clonal Cell Linesmentioning

confidence: 99%

A role for transcription from a piRNA cluster in de novo piRNA production

Kawaoka¹,

Mitsutake²,

Kiuchi³

et al. 2011

RNA

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PIWI-interacting RNAs (piRNAs) are at the heart of the nucleic acid-based adaptive immune system against transposons in animal gonads. To date, how the piRNA pathway senses an element as a substrate and how de novo piRNA production is initiated remain elusive. Here, by utilizing a GFP transgene, we screened and obtained clonal silkworm BmN4 cell lines producing massively amplified GFP-derived piRNAs capable of silencing GFP in trans. In multiple independent cell lines where GFP expression was silenced by the piRNA pathway, we detected a common transcript from an endogenous piRNA cluster, in which a part of the cluster is uniquely fused with an antisense GFP sequence. Bioinformatic analyses suggest that the fusion transcript is a source of GFP primary piRNAs. Our data implicate a role for transcription from a piRNA cluster in initiating de novo piRNA production against a new insertion.

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Bombyx small RNAs: Genomic defense system against transposons in the silkworm, Bombyx mori

Cited by 41 publications

References 59 publications

The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes

The ubiquitous hammerhead ribozyme

A role for transcription from a piRNA cluster in de novo piRNA production

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