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Published on: February 1, 2019
A large quantity of novel human antisense transcripts detected by LongSAGE
Xijin Ge1, Qingfa Wu, Yong-Chul Jung
1Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine 1001 University Place, Evanston, IL 60201 USA.
Bioinformatics (Oxford, England)
|August 10, 2006
Summary
Researchers identified novel human antisense transcripts using LongSAGE data, revealing their widespread presence in the human genome. This study enhances understanding of gene expression and regulation.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- LongSAGE (Long Serial Analysis of Gene Expression) technology offers high sensitivity and specificity for transcript detection and genome mapping.
- Antisense transcripts, originating from the opposite strand of known genes, play crucial roles in gene regulation.
- Previous studies have hinted at the existence of antisense transcripts, but comprehensive identification remained challenging.
Purpose of the Study:
- To identify novel human antisense transcripts by analyzing a large dataset of LongSAGE tags.
- To characterize the prevalence and expression levels of these antisense transcripts.
- To develop a database for identifying antisense SAGE tags.
Main Methods:
- Analysis of 632,813 unique human LongSAGE tags from public databases.
- Matching tags to the antisense strand of known mRNA sequences in the RefSeq database.
- Quantitative analysis of antisense transcript expression levels.
- Experimental validation of identified antisense transcripts.
- Construction of an antisense tag database.
Main Results:
- Identification of 45,321 tags corresponding to the antisense strand of 9,804 known mRNA sequences.
- Discovery that antisense transcripts are generally expressed at lower levels than their sense counterparts.
- Experimental confirmation of the presence of antisense transcripts detected by SAGE tags.
- Development of a searchable database for antisense SAGE tags.
Conclusions:
- SAGE data is a valuable resource for comprehensive identification of human antisense transcripts.
- Antisense transcripts are prevalent in the human genome, suggesting significant regulatory roles.
- The developed database facilitates further research into antisense transcript function and regulation.
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