Please use this identifier to cite or link to this item: https://doi.org/10.1101/gr.6018607
Title: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
Authors: Ruan, Y.
Hong, S.O.
Siew, W.C.
Kuo, P.C.
Xiao, D.Z.
Srinivasan, K.G.
Yao, F.
Chiou, Y.C.
Liu, J.
Ariyaratne, P.
Bin, W.G.W.
Kuznetsov, V.A.
Shahab, A.
Sung, W.-K. 
Bourque, G.
Palanisamy, N.
Wei, C.-L.
Issue Date: 2007
Source: Ruan, Y., Hong, S.O., Siew, W.C., Kuo, P.C., Xiao, D.Z., Srinivasan, K.G., Yao, F., Chiou, Y.C., Liu, J., Ariyaratne, P., Bin, W.G.W., Kuznetsov, V.A., Shahab, A., Sung, W.-K., Bourque, G., Palanisamy, N., Wei, C.-L. (2007). Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Research 17 (6) : 828-838. ScholarBank@NUS Repository. https://doi.org/10.1101/gr.6018607
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. ©2007 by Cold Spring Harbor Laboratory Press.
Source Title: Genome Research
URI: http://scholarbank.nus.edu.sg/handle/10635/38985
ISSN: 10889051
DOI: 10.1101/gr.6018607
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
There are no files associated with this item.

SCOPUSTM   
Citations

82
checked on Dec 7, 2017

WEB OF SCIENCETM
Citations

74
checked on Nov 22, 2017

Page view(s)

77
checked on Dec 11, 2017

Google ScholarTM

Check

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.