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RNA sequence analysis defines Dicer's role in mouse embryonic stem cells - PubMed

  • ️Mon Jan 01 2007

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells

J Mauro Calabrese et al. Proc Natl Acad Sci U S A. 2007.

Erratum in

  • Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):21021

Abstract

Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can be accounted for by six distinct miRNA loci. Four of these miRNA loci or their human homologues have demonstrated roles in cell cycle regulation or oncogenesis, suggesting that a major function of the miRNA pathway in ES cells may be to shape their distinct cell cycle. Forty-six previously uncharacterized miRNAs were identified, most of which are expressed at low levels and are less conserved than the set of known miRNAs. Low-abundance short RNAs matching all classes of repetitive elements were present in cells lacking Dicer, although the production of some SINE- and simple repeat-associated short RNAs appeared to be Dicer-dependent. These and other Dicer-dependent sequences resembled miRNAs. At a depth of sequencing that approaches the total number of 5' phosphorylated short RNAs per cell, miRNAs appeared to be Dicer's only substrate. The results presented suggest a model in which repeat-associated miRNAs serve as host defenses against repetitive elements, a function canonically ascribed to other classes of short RNA.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.

Conservation, expression, and repeat overlap of known and novel miRNA hairpins. (A) Conservation and ES cell expression of known and novel miRNA hairpins. The percentage of miRNA hairpins overlapping repeats is bracketed for three bins of conservation. The genomic locations of the chr2, 12, and X clusters are described

SI Table 7

. (B) Repeatmasker overlap of known and novel miRNA hairpins. Numbers refer to the total number of miRNA hairpins in each category. “Multiple” refers to those hairpins overlapping more than one class of repeat.

Fig. 2.
Fig. 2.

Analysis of highly repetitive novel sequences. (A) First nucleotide distribution of highly repetitive novel sequences (≥20 hits to the genome) compared with nonrepetitive novel sequences (<20 hits to the genome) and known miRNAs. (B) Length distribution of highly repetitive novel sequences compared with all nonrepetitive novel sequences. (C) Repeatmasker classification of highly repetitive novel sequences, represented as proportions of novel reads per library. The number of novel reads per library is in parentheses.

Fig. 3.
Fig. 3.

Description of Dicer-dependent novel sequences. (A) Length distribution of Dicer-dependent novel sequences compared with all other Dicer+/+ and Dicer−/− novel sequences. (B) First nucleotide distribution of Dicer-dependent novel sequences. (C) Two groups of Dicer-dependent sequences share sequence similarity. Shown are identified sequence motifs along with aligning sequences, total reads by library, number of genome matches, and overlapping repeats.

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