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Alu  elements are primate-specific repeats and represent the most abundant type of transposable elements (TE) in the human genome. Genome-wide analysis of the enrichment of histone post-translational modifications suggests that human  Alu  sequences could function as transcriptional enhancers; however, no functional experiments have evaluated the role of  Alu  sequences in the control of transcription  in situ . The present study analyses the regulatory activity of a human  Alu  sequence from the  AluSx  family located in the second intron of the long intergenic non-coding RNA  Linc00441 , found in divergent orientation to the  RB1  gene. We observed that the  Alu  sequence acts as an enhancer element based on reporter gene assays while CRISPR-Cas9 deletions of the  Alu  sequence in K562 cells resulted in a marked transcriptional upregulation of  Linc00441  and a decrease in proliferation. Our results suggest that an intragenic  Alu  sequence with enhancer activity can act as a transcriptional attenuator of its host lincRNA.

An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines