ArticleGenome research2007
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 95 citations in OpenAlex.
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- Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.PloS one · 2015Article
- Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites.Nucleic acids research · 2014Article
- Identification of cancer gene fusions based on advanced analysis of the human genome or transcriptome.Frontiers of medicine · 2013Review
- Cancer genome-sequencing study design.Nature reviews. Genetics · 2013Review
- Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis.Plant physiology · 2013Article
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- Detection of a common chimeric transcript between human chromosomes 7 and 16.Biology direct · 2012Article
- Understanding transcriptional regulation by integrative analysis of transcription factor binding data.Genome research · 2012Article
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- Modeling gene expression using chromatin features in various cellular contexts.Genome biology · 2012Article
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- ChimeraScan: a tool for identifying chimeric transcription in sequencing data.Bioinformatics (Oxford, England) · 2011Article
- Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.Cancer genetics · 2011Article
- Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.Genome research · 2011Article
- Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.Genome research · 2011Article
- Transcriptional consequences of genomic structural aberrations in breast cancer.Genome research · 2011Article
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
Abstract
Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5' and 3' transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.
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