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Regulating Pol III transcription to change Pol II transcriptome

The human genome harbors more than a million copies of Alu, a member of retrotransposons called short interspersed nuclear elements (SINEs).1 Alu is about 300 bp in length and originated from 7SL RNA, an RNA polymerase III (Pol III) transcript involved in protein transport. Accordingly, Alu is also transcribed by Pol III. However, most Alu copies are not occupied by the Pol III subunits,2 and the Alu RNA level is much lower than other Pol III transcripts, such as 7SL RNA, tRNAs, and 5S rRNA. Mutations in Alu copies, genomic position effects, and epigenetic silencing are thought to account for the limited Alu transcription, but the whole picture remains obscure.3 Interestingly, Alu RNA directly binds to Pol II and inhibits transcription of many protein-coding genes.4 Moreover, under the heat-shock condition, Alu transcription is upregulated while many Pol II genes are repressed, suggesting a role of Alu RNA in the heat-shock-induced global decrease in the Pol II activity.4