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Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22
Open accessAbstract
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.
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Self-citationUsing the transcriptome to annotate the genome
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Evolution and Functions of Long Noncoding RNAs
Ponting, C. P., Oliver, P. L., & Reik, W. (2009) · Cell · doi:10.1016/j.cell.2009.02.006 · Cited by 4,208
RNA regulation: A new genetics?
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Genome-wide Analysis of Alternative Pre-mRNA Splicing
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Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
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Analyzing Schizophrenia by DNA Microarrays
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Metadata
- Authors
- Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., Tammana, H., & Gingeras, T. R.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-03
- Volume
- 14
- Issue
- 3
- Pages
- 331-342
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2143593381
- Cited by
- 526
- References
- 3
- Type
- posted content
- Language
- en
- Open access
- bronze
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