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| Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22 |
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| Author(s): Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, Tammana H, Gingeras TR |
| Source: GENOME RESEARCH Volume: 14 Issue: 3 Pages: 331-342 Published: MAR 2004 |
| Times Cited: 277 References: 34 |
| Abstract: 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. |
| Document Type: Article |
| Language: English |
| Reprint Address: Kampa, D (reprint author), Affymetrix, Santa Clara, CA 95051 USA |
Addresses:
1. Affymetrix, Santa Clara, CA 95051 USA |
| Publisher: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2924 USA |
| Subject Category: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity |
| IDS Number: 780PB |
| ISSN: 1088-9051 |
| DOI: 10.1011/gr.2094104 |
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