Deletion of the sclerotome-enriched lncRNA PEAT augments ribosomal protein expression

Significance The majority of transcription generates noncoding RNAs, most of which are uncharacterized. Using RNA-seq on cultured mouse sclerotome, we identified PEAT , a long-noncoding RNA (lncRNA) adjacent to a key regulator of sclerotome, Pax1 . We deleted the entire PEAT -transcribed unit using CRISPR/Cas9 and analyzed RNA-seq from mutant embryos. While some lncRNAs regulate the expression of their proximal genes, our analysis showed Pax1 expression to be unchanged. However, we identified 60 ribosomal proteins with elevated expression, and found evidence that bone morphogenetic protein signaling is slightly elevated in PEAT mutants. This study reveals a role for the lncRNA PEAT in sclerotome development and shows next-generation sequencing to be a powerful tool to reveal surprising functions for lncRNAs.