Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

Kapranov, P., Drenkow, J., Cheng, J., Long, J., Helt, G., Dike, S., Gingeras, T. R. (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Research, 15 (7). pp. 987-997. ISSN 10889051 (ISSN) (Public Dataset)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/15998911
DOI: 10.1101/gr.3455305

Abstract

Recently, we mapped the sites of transcription across ∼30% of the human genome and elucidated the structures of several hundred novel transcripts. In this report, we describe a novel combination of techniques including the rapid amplification of cDNA ends (RACE) and tiling array technologies that was used to further characterize transcripts in the human transcriptome. This technical approach allows for several important pieces of information to be gathered about each array-detected transcribed region, including strand of origin, start and termination positions, and the exonic structures of spliced and unspliced coding and noncoding RNAs. In this report, the structures of transcripts from 14 transcribed loci, representing both known genes and unannotated transcripts taken from the several hundred randomly selected unannotated transcripts described in our previous work are represented as examples of the complex organization of the human transcriptome. As a consequence of this complexity, it is not unusual that a single base pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated. Some of these transcripts follow the canonical splicing rules, whereas others combine the exons of different genes or represent other types of noncanonical transcripts. These results have important implications concerning the correlation of genotypes to phenotypes, the regulation of complex interlaced transcriptional patterns, and the definition of a gene. ©2005 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: transcriptome article correlation analysis exon gene structure genetic code genetic transcription genomics genotype human medical technology nucleotide sequence phenotype priority journal RNA splicing Cell Line Gene Expression Profiling Humans Jurkat Cells Models Genetic Molecular Sequence Data Nucleic Acid Amplification Techniques Oligonucleotide Array Sequence Analysis Protein Isoforms Transcription Genetic Tumor Cells Cultured
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 2005
Date Deposited: 09 Mar 2012 21:38
Last Modified: 15 Jul 2013 14:34
PMCID: PMC1172043
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Dataset ID:
URI: http://repository.cshl.edu/id/eprint/25303

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