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.
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, P.H.S.
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Validation Study
MeSH terms
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Cell Line
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Cell Line, Tumor
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Chromosome Mapping / methods
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Chromosomes, Human, Pair 21 / genetics*
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Chromosomes, Human, Pair 22 / genetics*
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DNA, Neoplasm / genetics
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Gene Expression Profiling / methods
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Genes / genetics
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Genes, Neoplasm / genetics
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Humans
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Jurkat Cells / chemistry
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Jurkat Cells / metabolism
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Molecular Sequence Data
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Oligonucleotide Array Sequence Analysis / methods
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Oligonucleotide Probes / genetics
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RNA / genetics*
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RNA, Messenger / genetics
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Transcription, Genetic / genetics*
Substances
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DNA, Neoplasm
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Oligonucleotide Probes
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RNA, Messenger
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RNA
Associated data
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