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Description
ABI: Exon Splice Pattern Characterization of the \Vho1e mRNA
Transcri ptome
Synopsis: ~ext generation sequencing-by-synthesis technologies adapted for transcriptional profiling
applications have the potential to identify and differentiate all mR~ A splice variants in a
sample's transcriptome. while concurrently providing a direct quantitative measurement of their
steady state level. This proposal requests support to develop novel analytical methods that will
identify and align R~A sequencing tags that bridge exon splice junctions and accurately predict
mR.';"A structure with much greater sensitivity than is currently possible. The proposed methods
will characterize exon splice junctions directly by analyzing the nucleotide sequence of the tag in
comparison to the corresponding reference genome, using algorithms that do not rely on the existing
accuracy of mR~A structural annotation. ~ovel splice junctions will be identified and assessed
with the same efficiency as splice junctions that are already well characterized. The methods will
enable alternative mRNA splicing variants to be identified and quantified. Comparative tissue
analyses will be used as a test application of the analytical methods.
Intellectual Merit: Analytical and computational methods will be developed to interrogate the
mR~A transcriptome using next generation deep sequencing technologies. These computational
methods are:
• Identification of splice junction tags (tags that bridge exon junctions) and determination of
expression intensity levels for exons and mRNA splicing patterns genome-wide.
• Representation of the structure and expression intensity level of all exon splicing patterns
using Intensity-Weighted Splice Graph (WSG).
• An optimization algorithm to reconstruct different mRNA splice variants using vVSG.
• Approaches for analyzing tissue-specific splicing patterns and for identifying conserved 1Iltron/
exon sequences that regulate them.
The project assembles an interdisciplinary and collaborative team of scientists representing
computational genomics (Drs. Liu and Prins). statistical genomics (Drs. Bathke and Stromberg).
and functional genomics (Dr. MacLeod). Areas of individual expertise will be highly synergistic
for both the research and educational objectives of this proposal.
Status | Finished |
---|---|
Effective start/end date | 8/1/09 → 7/31/13 |
Funding
- National Science Foundation: $1,027,384.00
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Projects
- 3 Finished
-
ARRA: Exon Splice Pattern Characterization of the Whole mRNA Transcriptome
Liu, J. (PI), Bathke, A. (CoI), MacLeod, J. (CoI) & Stromberg, A. (CoI)
8/1/09 → 8/1/09
Project: Research project
-
ARRA: REU Exon Splice Pattern Characterization of the Whole mRNA Transcriptome
Liu, J. (PI), MacLeod, J. (CoI), Stromberg, A. (CoI) & Bathke, A. (Former CoI)
8/1/09 → 7/31/13
Project: Research project
-
ARRA: Exon Splice Pattern Characterization of the Whole mRNA Transcriptome
MacLeod, J. (PI)
8/1/09 → 7/31/13
Project: Research project