Endogenous siRNAs Derived from Transposons and mRNAs in
            <i>Drosophila</i>
            Somatic Cells

Ghildiyal, Megha; Seitz, Hervé; Horwich, Michael D.; Li, Chengjian; Du, Tingting; Lee, Soohyun; Xu, Jia; Kittler, Ellen L. W.; Zapp, Maria L.; Weng, Zhiping; Zamore, Phillip D.

doi:10.1126/science.1157396

Cited by 602 publications

(669 citation statements)

References 28 publications

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“…The endogenous siRNA pathway mediated by Dicer‐2 ( Dcr‐2 ) and Argonaute2 ( AGO2 ) have been shown to repress retrotransposon expression in Drosophila somatic cells. Previous studies have shown that AGO2 mutant flies or shRNA‐mediated depletion of AGO2 caused increased expression of retrotransposons in Drosophila brain and S2 cells (Czech et al ., 2008; Ghildiyal et al ., 2008; Li et al ., 2013). Thus, we depleted AGO2 in the fat body ( Cg‐gal4>AGO2 shRNA) by shRNA (mediated by Dicer‐1 ‐ AGO1 ) using two different fly RNAi lines (line 1: Bloomington Stock Center #34799, and line 2: Bloomington Stock Center #55672) that target different AGO2 sequences.…”

Section: Resultsmentioning

confidence: 99%

Age‐associated de‐repression of retrotransposons in the Drosophila fat body, its potential cause and consequence

et al. 2016

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SummaryEukaryotic genomes contain transposable elements (TE) that can move into new locations upon activation. Since uncontrolled transposition of TEs, including the retrotransposons and DNA transposons, can lead to DNA breaks and genomic instability, multiple mechanisms, including heterochromatin‐mediated repression, have evolved to repress TE activation. Studies in model organisms have shown that TEs become activated upon aging as a result of age‐associated deregulation of heterochromatin. Considering that different organisms or cell types may undergo distinct heterochromatin changes upon aging, it is important to identify pathways that lead to TE activation in specific tissues and cell types. Through deep sequencing of isolated RNAs, we report an increased expression of many retrotransposons in the old Drosophila fat body, an organ equivalent to the mammalian liver and adipose tissue. This de‐repression correlates with an increased number of DNA damage foci and decreased level of Drosophila lamin‐B in the old fat body cells. Depletion of the Drosophila lamin‐B in the young or larval fat body results in a reduction of heterochromatin and a corresponding increase in retrotransposon expression and DNA damage. Further manipulations of lamin‐B and retrotransposon expression suggest a role of the nuclear lamina in maintaining the genome integrity of the Drosophila fat body by repressing retrotransposons.

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Section: Resultsmentioning

confidence: 99%

Age‐associated de‐repression of retrotransposons in the Drosophila fat body, its potential cause and consequence

et al. 2016

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“…In the light of the emerging evidence for regulatory roles of pseudogenes and transposon (Grandbastien et al, 2005;Czech et al, 2008;Ghildiyal et al, 2008;Kawamura et al, 2008;Tam et al, 2008;Watanabe et al, 2008) these findings might point to functions of these genomic elements in stress response. Alternatively, since transcriptional silencing of transposons involves small RNAs (Weil and Martienssen, 2008), the activation of these transcripts might reflect general effects of abiotic stress on the small RNA complement of the plant.…”

Section: Stress-induced Changes In the Arabidopsis Transcriptome 1069mentioning

confidence: 99%

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

et al. 2009

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SUMMARYThe responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.

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“…The production of such complex populations of small RNA sequences from a single precursor is a hallmark of endogenous siRNAs ( Fig. 1C; Czech et al 2008;Ghildiyal et al 2008;Okamura et al 2008;Kim et al 2009). …”

Section: Discovery Of Nematostella Mirnas and Sirnasmentioning

confidence: 99%

Cnidarian microRNAs frequently regulate targets by cleavage

et al. 2014

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In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA ''seed'') to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.

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Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

Cited by 602 publications

References 28 publications

Age‐associated de‐repression of retrotransposons in the Drosophila fat body, its potential cause and consequence

Age‐associated de‐repression of retrotransposons in the Drosophila fat body, its potential cause and consequence

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

Cnidarian microRNAs frequently regulate targets by cleavage

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