A Comprehensive Analysis of Cell Type–Specific Nuclear RNA From Neurons and Glia of the Brain

Abstract

Background Studies in psychiatric genetics have identified over 100 loci associated with disease risk, yet many of these loci are distant from protein coding genes. Recent characterization of the transcriptional landscape of cell lines and whole tissues has suggested widespread transcription in both coding and non-coding regions of the genome, including differential expression from loci that produce regulatory non-coding RNAs which function within the nucleus; however, the nuclear transcriptome of specific cell types in the brain has not been previously investigated. Methods Here we have defined the nuclear transcriptional landscape of the three major cellular divisions of the nervous system using flow sorting of genetically labeled nuclei from bacTRAP mouse lines. This was followed by characterization of the unique expression of coding, non-coding and intergenic RNAs in the mature mouse brain with RNAseq and validation with independent methods. Results Our findings reveal diverse expression across the cell-types of all classes of RNAs, including long non-coding RNAs – several of which were confirmed as highly enriched in the nuclei of specific cell-types using anatomical methods. Finally, we also discovered several examples of cell-type specific expression of tandem gene fusions, and report the first cell-type specific expression of circular RNAs, notably a neuron-specific and nuclear-enriched RNA arising from the gene Hnrnpu. Conclusion These data will provide an important resource for studies evaluating the function of a variety of ncRNAs in the brain, including those that may play a role in psychiatric disease.

GPR37L1 modulates seizure susceptibility: Evidence from mouse studies and analyses of a human GPR37L1 variant

“…GPR37L1 is an orphan G protein-coupled receptor (GPCR) expressed predominantly in the brain, with highest expression in astrocytes and Bergmann glia, as well as expression in some populations of neurons and oligodendrocytes 14–16, 38–40 . While Gpr37L1 has been shown to play a role in postnatal cerebellar development in a mouse model 17 , the overall function of this receptor is unknown.…”

“…GPR37L1 is highly expressed in the Bergmann glia of the cerebellum 14; 17 and mice lacking Gpr37L1 show alterations in postnatal cerebellar development 17 . GPR37L1 is also highly expressed in astrocytes and certain populations of neurons, and both GPR37 and GPR37L1 are widely expressed throughout the brain 14–16; 38–40 Thus, it is likely that GPR37L1 and GPR37 have additional functions outside the cerebellum and dopaminergic system, respectively. We and others have shown that expression of GPR37L1 and/or GPR37 can mediate cytoprotective effects in vitro 25; 26 Therefore, it is possible that these receptors play important roles in mediating protective effects following insult or injury in vivo .…”

Astrocytes locally translate transcripts in their peripheral processes

“…FISH was performed on 14-μm slide-mounted cryosections after 4% PFA fixation of virally injected animals. Custom digoxigenin-labeled antisense probes were hybridized overnight, washed, H 2 O 2 -blocked, Dig-antibodylabeled, and detected via Tyramide Signal Amplification Cyanine 3 Tyramide (PerkinElmer #NEL704A001KT) as described previously (54). IF was subsequently performed.…”

“…2500, for a total of 195 M 50-bp reads across the 12 samples. Reads were analyzed as described previously (54). Raw and analyzed RNA-sequencing data are also available at the Gene Expression Omnibus, accession no.…”

Sequencing on the SOLiD 5500xl System – in-depth characterization of the GC bias

“…These intergenic regions might be highly relevant for studies into genetic and epigenetic mechanisms of neuropsychiatric disease mechanisms, since e.g., relevant GWAS risk loci often map to intergenic regions. 16 …”