Abstract
Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the Polr3e gene, encoding an RNA polymerase III (Pol III) subunit, is conserved in mammals and highly occupied by Pol III. Using a fluorescence assay, CRISPR/Cas9-mediated deletion of the MIR in mouse embryonic stem cells, and chromatin immunoprecipitation assays, we show that the MIR affects Polr3e expression through transcriptional interference. Our study reveals a mechanism by which a Pol II gene can be regulated at the transcription elongation level by transcription of an embedded antisense Pol III gene.
Highlights
In eukaryotes, RNA polymerase II (Pol II) is responsible for transcription of all of the mRNA-encoding genes as well as most genes encoding small nuclear RNA and microRNAs
chromatin immunoprecipitation (ChIP)-seq (ChIP combined with high-throughput sequencing) data obtained from mouse livers reveal that this mammalian interspersed repeat (MIR) is as highly occupied by polymerase III (Pol III) as a transfer RNA (tRNA) Leu gene located upstream of the Polr3e transcription start site (TSS) (Fig. 1A)
The high Pol III occupancy of this particular MIR is in contrast to the low occupancy of most short interspersed nuclear elements (SINEs) and prompted us to search for its presence in other species
Summary
RNA polymerase II (Pol II) is responsible for transcription of all of the mRNA-encoding genes as well as most genes encoding small nuclear RNA (snRNA) and microRNAs. We examined the role of a member of the mammalian interspersed repeat (MIR) family, an ancient family of tRNA-derived SINEs that were amplified before the mammalian radiation (Smit and Riggs 1995). This MIR is nested in antisense orientation within the first intron of the Polr3e gene, which codes for one of the Pol III subunits. We show that this arrangement is conserved in different mammalian species and that it directly impacts on Pol II transcription elongation through the Polr3e gene. The Pol III transcribed MIR can contribute to regulation of a Pol III subunit-encoding gene
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