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Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Actinomyces naeslundii is a pioneer of the oral cavity and forms a biofilm on the tooth's surface. Most bacteria require iron for survival and in pathogenic bacteria iron availability regulates virulence gene expression. Metal-dependent repressors control gene expression involved in metal transport and uptake including siderophores. Siderophores are small molecules synthesized by bacteria and fungi to acquire iron. The A. naeslundii genome was searched for a gene encoding a metal-dependent repressor. Actinomyces metal-dependent repressor or amdR was identified. The AmdR protein was examined for its ability to bind to the promoter sequence of a gene encoding the siderophore uptake (sid gene). According to gel shift assays, AmdR binds to the sid gene promoter sequences. In the authors' model, when iron is available AmdR binds to the sid promoter and represses sid gene expression. To further explore the role of AmdR, an amdR-defective strain of A. naeslundii was constructed and biofilm formation and siderophore production were evaluated. When iron is removed from the medium A. naeslundii increases biofilm and siderophore production. However, amdR-defective A. naeslundii is less sensitive to metal ion concentrations in the growth medium.