In total, we detected 222 lncRNAs differentially expressed between ASD and control samples (fold change
0.05). Eighty-two of these were unique to the prefrontal cortex, and 143 were unique to the cerebellum (Fig. ). The majority of differentially expressed lncRNAs in ASD were from intergenic regions (~60 %), antisense to protein-coding loci (~15 %), or within introns of protein-coding genes (~10 %), with the others representing overlapping transcripts from exons or introns in both sense and antisense directions. This distribution was not significantly different from the distribution of all lncRNAs detected by the array (Supplementary Data—Additional File 1
, Fig. 1). We confirmed a select number of the most highly differentially expressed lncRNAs between autism and controls by qRT-PCR analysis (Supplementary Data—Additional File 1
, Fig. 2).
Summary of differentially expressed lncRNAs and mRNAs. Asterisk, three shared lncRNAs; caret, 99 shared lncRNAs
Almost 50 % of differentially expressed lncRNAs map to within 50 kilobases (kb) of an annotated gene, and greater than 90 % map within 500 kb of a known gene (Supplementary Data—Additional File 1
, Fig. 3). Mapping all differentially expressed lncRNAs to the nearest genes identified 381 protein-coding loci under putative cis
-regulatory control by these lncRNAs. The ontologies of those loci implicated two functions: cerebral cortex cell migration and targets of microRNAs mir-103/107 (Table ). These results are intriguing given that the prevailing cellular model of autism is a defect in neuronal connectivity (Geschwind and Levitt 2007
) and that mir-103/107 has previously been implicated in CNS development (Moncini et al. 2011
), Alzheimer’s disease (Nelson and Wang 2010
), and schizophrenia (Santarelli et al. 2011
). Eleven of these genes near differentially expressed lncRNAs have previously been implicated in ASD, and 18 have previously been shown to exhibit differential expression in ASD brain (Supplementary Data—Additional File 1
, Table 4).
Gene ontology analysis of 381 mRNA loci nearby differentially expressed lncRNAs
Ninety of the differentially expressed lncRNAs are oriented in or around a known protein-coding region (i.e., not intergenic). Of these, three are known imprinted loci in humans (C9orf85, SLC4A2, and UBE3A). Interestingly, UBE3A is implicated in the genomic imprinting disorder Angelman syndrome, which shares many features with ASD (Bonati et al. 2007
). Surprisingly, however, only 3 of these 90 genes are also differentially expressed (RBM8a, ARL17A, and KLF6), suggesting perhaps more complex mechanisms for many of these lncRNAs than simple cis
Our array also contained probes for known protein-coding transcripts, of which we detected 355 genes differentially expressed between ASD and controls, which were enriched for the process of alternative splicing (Supplementary Data—Additional File 1
, Table 5). This finding is in agreement with a recent large transcriptome study in autistic brains by Voineagu et al., where they demonstrated dysregulated splicing of A2BP1
-dependent exons in ASD brains using RNA-seq (Voineagu et al. 2011
Because our samples from the prefrontal cortex and cerebellum were from the same patients, we also had the ability to compare intra-individual differences in expression of both genes and lncRNAs between these regions. We detected almost 2,000 genes differentially expressed in the control prefrontal cortex versus the control cerebellum, which were highly enriched for gene ontology terms related to synaptogenesis (Supplementary Data—Additional File 1
, Table 6), but only 322 genes differentially expressed between the ASD prefrontal cortex and cerebellum (Fig. ). These results are also in agreement with the study by Voineagu and colleagues, where they observed more transcriptional homogeneity in ASD brains (Voineagu et al. 2011
). In light of this, then, we were intrigued to find that the number of lncRNAs differentially expressed within control brains was also much greater than lncRNAs differentially expressed within autism brains (1,375 lncRNAs versus 236 lncRNAs, respectively).