Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

TLDR

Novel transcripts were characterized by their proximity to known genes, size, coding potential, and antisense orientation to intronic sequences. High‑density array analysis of chromosomes 21 and 22 showed that only ~31% of transcribed nucleotides correspond to annotated genes, while the remaining ~49% represent novel, cell‑line‑specific transcripts—126 of which were verified by RT‑PCR at a 65% success rate—indicating that the human gene count may need to be revised.

Abstract

In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density oligonucleotide arrays on cytosolic poly(A) + RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas an additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and up to 21% of known genes have only a single isoform based on exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with an identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of any known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation in expression than the well-characterized genes. Novel transcripts were further characterized based on their distance to annotations, transcript size, coding capacity, and identification as antisense to intronic sequences. By RT-PCR, 126 novel transcripts were independently verified, resulting in a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for “gene” to encompass these growing, novel classes of RNA transcripts in the human genome.