Repression of the memory suppressor gene histone deacetylase 2 ( Hdac2 ) in mice elicits cognitive enhancement, and drugs that block HDAC2 catalytic activity are being investigated for treating disorders affecting memory. Currently available compounds that target HDAC2 are not specific to the HDAC2 isoform, and have short half-lives. Antisense oligonucleotides (ASOs) are a class of drugs that base pair with RNA targets and exhibit extremely long-lasting, specific inhibition relative to small molecule drugs. We utilized an ASO to reduce Hdac2 messenger RNA (mRNA) quantities, and explored its longevity, specificity, and mechanism of repression. A single injection of the Hdac2 -targeted ASO in the central nervous system diminished Hdac2 mRNA levels for at least 4 months in the brain, and knockdown of this factor resulted in significant memory enhancement for 8 weeks in mice. RNA-seq analysis of brain tissues revealed that the ASO repression was specific to the Hdac2 isoform relative to other classical Hdac genes, and caused alterations in levels of other memory-associated mRNAs. In cultured neurons, we observed that the Hdac2 -targeted ASO suppressed Hdac2 mRNA and an Hdac2 non-coding regulatory extra-coding RNA (ecRNA). The ASO not only triggered a reduction in mRNA levels, but also elicited direct transcriptional suppression of the Hdac2 gene through blocking RNA polymerase II elongation. These findings suggest transcriptional suppression of the target gene as a novel mechanism of action of ASOs, and opens up the possibility of using ASOs to achieve lasting gene silencing in the brain without altering the nucleotide sequence of a gene.

An antisense oligonucleotide leads to suppressed transcriptional elongation of Hdac2 and long-term memory enhancement