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Pan-genome isolation of low abundance transcripts using SAGE tag
Yeong Cheol Kim1, Yong-Chul Jung, Zhenyu Xuan
1Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA.
FEBS Letters
|November 23, 2006
Summary
Serial analysis of gene expression (SAGE) effectively identifies novel, low-abundance transcripts. However, SAGE tag mis-priming can lead to incorrect gene mapping, highlighting transcript sequence similarity issues.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Serial analysis of gene expression (SAGE) is a sensitive technique for detecting low-abundance transcripts.
- A significant portion of human SAGE tags represent novel, low-abundance transcripts of unknown function.
Purpose of the Study:
- To investigate the utility of the GLGI method for identifying novel transcripts from human X chromosome-specific SAGE tags.
- To analyze the origin and mapping of 3' ESTs generated from low-copy SAGE tags.
Main Methods:
- Utilized the GLGI (generation of longer 3' EST from SAGE tag for gene identification) method.
- Converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3' ESTs.
- Mapped generated 3' ESTs to the human genome.
Main Results:
- Identified 3418 unique 3' ESTs, with 46% being novel and originating from low-abundance transcripts.
- Observed that most 3' ESTs mapped to genomic regions outside the X chromosome.
- Determined that SAGE tag mis-priming to non-parent transcripts, driven by sequence similarity, caused incorrect mapping.
Conclusions:
- SAGE tags can efficiently isolate novel, low-abundance transcripts.
- Mis-priming due to transcript sequence similarity is a significant factor affecting accurate gene identification with SAGE.
- Further refinement of SAGE-based methods is needed to overcome mis-priming artifacts and ensure accurate transcript mapping.
