RT Journal
A1 Kampa, Dione
A1 Cheng, Jill
A1 Kapranov, Philipp
A1 Yamanaka, Mark
A1 Brubaker, Shane
A1 Cawley, Simon
A1 Drenkow, Jorg
A1 Piccolboni, Antonio
A1 Bekiranov, Stefan
A1 Helt, Gregg
A1 Tammana, Hari
A1 Gingeras, Thomas R.
T1 Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
JF Genome Research 
JO Genome Research 
YR 2004 
FD March 01 
VO 14 
IS 3 
SP 331 
OP 342 
DO 10.1101/gr.2094104 
UL http://genome.cshlp.org/content/14/3/331.abstract 
AB 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.