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Silas et al. discover that certain classes of the Cas1gene are fused to a reverse transcriptase gene (RT-Cas1) (see the Perspective by Sontheimer and Marraffini). These RT-Cas1 proteins are able to capture and directly incorporate both DNA and RNA into CRISPR loci. RT-Cas1 systems could be effective against parasitic RNA species, or even to modulate bacterial gene expression.