Pan-genome isolation of low abundance transcripts using SAGE tag

Kim, Y. C., Jung, Y. C., Xuan, Z., Dong, H., Zhang, M. Q., Wang, S. M. (December 2006) Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters, 580 (28-29). pp. 6721-6729. ISSN 0014-5793

URL: http://www.ncbi.nlm.nih.gov/pubmed/17113583
DOI: 10.1016/j.febslet.2006.11.013

Abstract

The SAGE (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human SAGE tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3' EST from SAGE tag for gene identification), we converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3' ESTs. We identified 3418 unique 3' ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3' ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3' ESTs were isolated by SAGE tag mis-priming to the non-parent transcripts. Replacing SAGE tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming. (c) 2006 Federation of European Biochemical Societies.

Item Type: Paper
Uncontrolled Keywords: transcript low abundance SAGE tag 3 EST Predicted Protein Sequences Gene Expression Serial Analysis Functional Annotation IDENTIFICATION CDNAS Microarray DISCOVERY Databases NUMBER
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > databases > databases
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: December 2006
Date Deposited: 13 Dec 2011 15:22
Last Modified: 01 Mar 2013 15:53
PMCID: PMC1791009
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22838

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