The mouse alpha and beta cell transcriptomes reveal unique beta cell-specific lncRNAs. Mouse islet lncRNAs demonstrate significant enrichment for binding by the beta cell-specific transcription factors PDX1 (A) and NKX6.1 (B), are enriched for H3K4me1 and H3K4me3 markers of transcriptionally active loci (C) and are co-regulated with their nearest protein-coding neighbor (D). This is illustrated by lncRNAs adjacent to Nkx6.1 (E) and Pparg (F), which are co-enriched in mouse beta cells with these protein-coding genes and strongly associate with binding of beta cell-specific transcription factors. Overnight stimulation of mouse islets with 16.8 mM glucose strongly regulates a subset of lncRNAs in comparison to protein-coding transcripts (G) as illustrated by lncRNAs that are significantly up regulated by glucose at chromosome X (H), 8 (I) and 12 (J) or down regulated by glucose at chromosome 16 (K). ChIP-Seq and H3K4 data are from [38, 45, 48, 69]. Numbers inside the grey boxes refer to lncRNA coordinates and correspond to Additional file 11.