Abstract
In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the noncanonical Cid14 poly(A) polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5' uracil, and we argue these are loaded most efficiently into Argonaute. In wild-type cells most sRNAs match to repeated regions of the genome, whereas in cid14Delta cells the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Argonaute Proteins
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Cell Cycle Proteins / genetics
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Cell Cycle Proteins / metabolism
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Centromere / genetics
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DNA, Antisense / genetics
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Gene Deletion
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Genome, Fungal / genetics
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Histone-Lysine N-Methyltransferase
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Methyltransferases / genetics
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Methyltransferases / metabolism
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Nucleotides / genetics
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Polynucleotide Adenylyltransferase / genetics
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Polynucleotide Adenylyltransferase / metabolism
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Protein Binding
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RNA, Ribosomal / genetics
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RNA, Small Interfering / genetics*
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RNA-Binding Proteins
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Schizosaccharomyces / enzymology*
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Schizosaccharomyces / genetics*
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Schizosaccharomyces pombe Proteins / genetics
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Schizosaccharomyces pombe Proteins / metabolism
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Serine Endopeptidases / metabolism*
Substances
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Ago1 protein, S pombe
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Argonaute Proteins
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Cell Cycle Proteins
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DNA, Antisense
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Nucleotides
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RNA, Ribosomal
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RNA, Small Interfering
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RNA-Binding Proteins
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Schizosaccharomyces pombe Proteins
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Methyltransferases
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Histone-Lysine N-Methyltransferase
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clr4 protein, S pombe
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Cid14 protein, S pombe
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Polynucleotide Adenylyltransferase
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Serine Endopeptidases
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tunicate retinoic acid-inducible modular protease