C10567: The Antisense Transcriptomes of Human Cells - ASSAGE (Asymmetric Strand Specific Analysis of Gene Expression)Value Proposition:
• Novel method to determine DNA strand origin
• Combination method which includes the quantitation of both sense and antisense transcripts
• This method can be utilized from expressed genes at the global level
• The method has been optimized to identify DNA strand origins from the entire transcriptome
Technical Details:
BACKGROUND
Serial analysis of gene expression (SAGE) is a method for comprehensive analysis of gene expression patterns. SAGE is a JHU derived method to give scientists an overview of a cell’s complete gene activity. It works by capturing RNAs, identifying them and counting them. By comparing different types of cells, the researchers hope to generate profiles that will help them understand healthy cells and what goes wrong during diseases.
TECHNOLOGY
Related to the SAGE technology, is a method to identify the DNA strand of origin for any RNA transcript and to additionally quantify the number of sense and antisense transcripts from expressed genes at the global level. JHU scientists have developed a novel method called ASSAGE (Asymmetric Strand Specific Analysis of Gene Expression). This method utilizes bisulfate treatment of RNA to change all cytidine residues to uridine. Using this method, the bisulfate treated RNA molecule can only match with one of two possible DNA strands. cDNA is generated from bisulfate treated RNA followed by sequencing of the RT-PCR product to establish strand origin. This method has been adapted to identify DNA strand origins for the entire transcriptome and additionally provide transcript quantities.
The developed method was used in five cell types to quantify sense genes (S), antisense genes (AS), and transcripts which contain both sense and antisense tags (SAS). These three transcript types were identified in all five cell types with similar overall proportions; however, the distribution of sense and antisense for the five cell types was distinct and non-random.
Looking for Partners:
Commercially, this invention may be developed as a kit/service to determine strand origin and quantify transcripts. There is currently a lack of commercially available research tools to routinely assess the expression of sense and antisense RNAs in an efficient and cost effective manner.
Publications/Associated Cases:
He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N., & Kinzler, K. W. (2008). The antisense transcriptomes of human cells. Science, 322(5909), 1855-1857.
