Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22

In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density Oligonucleotide arrays oil cytosolic poly(A)(+) RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas all additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and LIP to 21% of known genes have only a single isoform based oil exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with all identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of ally known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation ill expression than the well-characterized genes. Novel transcripts were further characterized based oil 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 ill a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and all alternative term for gene to encompass these growing, novel classes of RNA transcripts in the human genome.