The long noncoding RNA Pnky is a trans-acting regulator of cortical development in vivo

While it is now appreciated that certain long noncoding in vivo, particularly with genetic strategies that establish cis versus trans mechanisms.  Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2.  Here we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination.  Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene.  Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo.  Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans. Set 1: Differential expression of acutely-dissected cortical tissue from E12.5 embryos. Biological triplicate samples of Pnky(fl/fl);Emx1-Cre and controls. Set 2: Differential expression in cultured NSCs performed by dissecting cortex from E12.5 Pnky(+/+), Pnky(fl/fl), and Pnky(fl/fl);BAC-Pnky mice in biological triplicate. Recombination was induced by Ad:Cre and cultured for 3 days prior to RNA extraction. Group-specific condition effects were analyzed by RNA-seq.