The human salivary RNA transcriptome revealed by massively parallel sequencing.

BACKGROUND: Evaluation of the salivary transcriptome is an emerging diagnostic technology with discriminatory power for disease detection. This study explored massively parallel sequencing for providing nucleotide-level sequence information for each RNA in saliva.
METHODS: Transcriptome profiling with the SOLiD™ system was applied to RNA isolated from unstimulated cell-free saliva (CFS) and whole saliva (WS) from healthy human volunteers. Sequenced reads were aligned to human genome build 18 and the Human Oral Microbiome Database (HOMD).
RESULTS: Massively parallel sequencing enabled the acquisition of complete sequence information for each nucleotide position of the human salivary transcriptome through alignment to multiple sequence databases. Approximately 20%-25% of the sequenced reads from CFS aligned to the human genome, and approximately 30% of the sequenced reads aligned to the HOMD. We detected the expression of >4000 coding and noncoding genes in CFS and WS. Gene expression at different genome loci showed that the structural integrity of the transcripts for the annotated genes was preserved in saliva.
CONCLUSIONS: A single measurement provided RNA sequence information of gene transcript abundance for both coding and noncoding RNAs and identified sequences from >400 different microbial species within a single sample. Contrary to previous data suggesting that salivary RNA is highly fragmented, in our study the structural integrity of RNA was preserved. The high degree of sequence alignment to annotated exons and introns for each of the respective reference genomes, with sequence coverage spanning the full length of the genes, provides strong evidence that the salivary transcriptome is a complex RNA network.