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

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. (2004) Novel RNAs identified from a in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research, 14 (3). pp. 331-342. ISSN 10889051 (ISSN) (Public Dataset)

DOI: 10.1101/gr.2094104


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. © 2004 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: antisense oligonucleotide DNA messenger RNA nucleotide polyadenylated RNA RNA article cell line cell specificity chromosome 21 chromosome 22 controlled study DNA microarray exon expressed sequence tag gene expression genetic code genetic identification human human cell human chromosome human genome intron priority journal reverse transcription polymerase chain reaction RNA analysis RNA transcription sequence analysis chemistry chromosome map gene gene expression profiling genetic transcription genetics leukemia cell line metabolism methodology molecular genetics oligonucleotide probe tumor cell line tumor gene validation study Cell Line Tumor Chromosome Mapping Chromosomes Human, Pair 21 Chromosomes Human, Pair 22 DNA, Neoplasm Genes Genes Neoplasm Humans Jurkat Cells Molecular Sequence Data Oligonucleotide Array Sequence Analysis Oligonucleotide Probes RNA, Messenger Transcription Genetic
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 2004
Date Deposited: 08 Mar 2012 17:42
Last Modified: 15 Jul 2013 15:14
PMCID: PMC353210
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