Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA

Ingela Djupedal, Isabelle C. Kos-Braun, Rebecca A. Mosher, Niklas Soderholm, Femke Simmer, Thomas J. Hardcastle, Aurelie Fender, Nadja Heidrich, Alexander Kagansky, Elizabeth Bayne, E. Gerhart H. Wagner, David C. Baulcombe, Robin C. Allshire, Karl Ekwall

    Research output: Contribution to journalArticle

    43 Citations (Scopus)

    Abstract

    The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009

    Original languageEnglish
    Pages (from-to)3832-3844
    Number of pages13
    JournalEMBO Journal
    Volume28
    Issue number24
    DOIs
    Publication statusPublished - 16 Dec 2009

    Cite this

    Djupedal, I., Kos-Braun, I. C., Mosher, R. A., Soderholm, N., Simmer, F., Hardcastle, T. J., ... Ekwall, K. (2009). Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO Journal, 28(24), 3832-3844. https://doi.org/10.1038/emboj.2009.351
    Djupedal, Ingela ; Kos-Braun, Isabelle C. ; Mosher, Rebecca A. ; Soderholm, Niklas ; Simmer, Femke ; Hardcastle, Thomas J. ; Fender, Aurelie ; Heidrich, Nadja ; Kagansky, Alexander ; Bayne, Elizabeth ; Wagner, E. Gerhart H. ; Baulcombe, David C. ; Allshire, Robin C. ; Ekwall, Karl. / Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. In: EMBO Journal. 2009 ; Vol. 28, No. 24. pp. 3832-3844.
    @article{cbc4319305304861988bea892d610356,
    title = "Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA",
    abstract = "The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009",
    author = "Ingela Djupedal and Kos-Braun, {Isabelle C.} and Mosher, {Rebecca A.} and Niklas Soderholm and Femke Simmer and Hardcastle, {Thomas J.} and Aurelie Fender and Nadja Heidrich and Alexander Kagansky and Elizabeth Bayne and Wagner, {E. Gerhart H.} and Baulcombe, {David C.} and Allshire, {Robin C.} and Karl Ekwall",
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    Djupedal, I, Kos-Braun, IC, Mosher, RA, Soderholm, N, Simmer, F, Hardcastle, TJ, Fender, A, Heidrich, N, Kagansky, A, Bayne, E, Wagner, EGH, Baulcombe, DC, Allshire, RC & Ekwall, K 2009, 'Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA', EMBO Journal, vol. 28, no. 24, pp. 3832-3844. https://doi.org/10.1038/emboj.2009.351

    Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. / Djupedal, Ingela; Kos-Braun, Isabelle C.; Mosher, Rebecca A.; Soderholm, Niklas; Simmer, Femke; Hardcastle, Thomas J.; Fender, Aurelie; Heidrich, Nadja; Kagansky, Alexander; Bayne, Elizabeth; Wagner, E. Gerhart H.; Baulcombe, David C.; Allshire, Robin C.; Ekwall, Karl.

    In: EMBO Journal, Vol. 28, No. 24, 16.12.2009, p. 3832-3844.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA

    AU - Djupedal, Ingela

    AU - Kos-Braun, Isabelle C.

    AU - Mosher, Rebecca A.

    AU - Soderholm, Niklas

    AU - Simmer, Femke

    AU - Hardcastle, Thomas J.

    AU - Fender, Aurelie

    AU - Heidrich, Nadja

    AU - Kagansky, Alexander

    AU - Bayne, Elizabeth

    AU - Wagner, E. Gerhart H.

    AU - Baulcombe, David C.

    AU - Allshire, Robin C.

    AU - Ekwall, Karl

    PY - 2009/12/16

    Y1 - 2009/12/16

    N2 - The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009

    AB - The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 50-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1D cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity. The EMBO Journal (2009) 28, 3832-3844. doi: 10.1038/emboj.2009.351; Published online 26 November 2009

    U2 - 10.1038/emboj.2009.351

    DO - 10.1038/emboj.2009.351

    M3 - Article

    VL - 28

    SP - 3832

    EP - 3844

    JO - EMBO Journal

    JF - EMBO Journal

    SN - 0261-4189

    IS - 24

    ER -

    Djupedal I, Kos-Braun IC, Mosher RA, Soderholm N, Simmer F, Hardcastle TJ et al. Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO Journal. 2009 Dec 16;28(24):3832-3844. https://doi.org/10.1038/emboj.2009.351