Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs.

Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional. Here we directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project. Furthermore, using de novo transcriptome assembly of this RNA-seq data, we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell, significantly expanding upon prior lincRNA annotation sets. These lincRNAs are specifically regulated and conserved rather than being the product of transcriptional noise. In addition, lincRNAs are strongly enriched for trait-associated SNPs suggesting a new mechanism by which intergenic trait-associated regions may function. These findings will enable the discovery and interrogation of novel intergenic functional elements.

A Genetic Interaction Map of Insulin Production Identifies Mfi as an Inhibitor of Mitochondrial Fission.

Insulin production by the pancreatic ß cell is critical for the glucose homeostasis of the whole organism. Although the transcription factors required for insulin production are known, the upstream pathways that control insulin production are less clear. To further elucidate this regulatory network, we created a genetic interaction map of insulin production by performing ∼20,000 pairwise RNA interference knockdowns of insulin promoter regulators. Our map correctly predicted known physical complexes in the electron transport chain and a role for Spry2 in the unfolded protein response. To further validate our map, we used it to predict the function of an unannotated gene encoding a 37-kDa protein with no identifiable domains we have termed mitochondrial fission factor interactor (Mfi). We have shown that Mfi is a binding partner of the mitochondrial fission factor and that Mfi inhibits dynamin-like protein 1 recruitment to mitochondria. Our data provide a resource to understand the regulatory network of insulin promoter activity.

Research resource: RNA-Seq reveals unique features of the pancreatic ß-cell transcriptome.

The pancreatic ß-cell is critical for the maintenance of glycemic control. Knowing the compendium of genes expressed in ß-cells will further our understanding of this critical cell type and may allow the identification of future antidiabetes drug targets. Here, we report the use of next-generation sequencing to obtain nearly 1 billion reads from the polyadenylated RNA of islets and purified ß-cells from mice. These data reveal novel examples of ß-cell-specific splicing events, promoter usage, and over 1000 long intergenic noncoding RNA expressed in mouse ß-cells. Many of these long intergenic noncoding RNA are ß-cell specific, and we hypothesize that this large set of novel RNA may play important roles in ß-cell function. Our data demonstrate unique features of the ß-cell transcriptome.