Simultaneous detection and relative quantification of coding and non-coding RNA using a single sequencing reaction

The ability to compare the abundance of one RNA molecule to another is a crucial step for understanding how gene expression is modulated to shape the transcriptome landscape. However, little information is available about the relative expression of the different classes of coding and non-coding RNA or even between RNA of the same class. In this study, we present a complete portrait of the human transcriptome that depicts the relationship of all classes of non-ribosomal RNA longer than sixty nucleotides. The results show that the most abundant RNA in the human rRNA-depleted transcriptome is tRNA followed by spliceosomal RNA. Surprisingly, the signal recognition particle RNA 7SL by itself occupied 8% of the ribodepleted transcriptome producing a similar number of transcripts as that produced by all snoRNA genes combined. In general, the most abundant RNA are non-coding but many more protein coding than non-coding genes produce more than 1 transcript per million. Examination of gene functions suggests that RNA abundance reflects both gene and cell function. Together, the data indicate that the human transcriptome is shaped by a small number of highly expressed non-coding genes and a large number of moderately expressed protein coding genes that reflect cellular phenotypes. Overall design: RNA was isolated from SKOV3ip1 and INOF human cell lines and selected with different methods. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.