Analysis of DNA strand-specific differential expression with high density tiling microarrays

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• DNA microarray technology enables genome-wide analysis of DNA structure and dynamics.
• Expression microarrays (EMA) analyze differential gene expression using probes for annotated open reading frames (ORF).
• Tiling microarrays (TMA) offer higher probe density and unbiased genome-wide coverage.

Purpose of the Study:

• To develop a protocol for quantitative, strand-specific differential expression analysis using high-resolution tiling microarrays (TMA).
• To compare the efficiency of TMAs with EMAs for gene expression analysis.
• To detect and quantify non-annotated and antisense transcripts.

Main Methods:

• Filtered probes from Affymetrix Genechip Yeast Genome 2.0 (EMA) and GeneChip S. pombe 1.0FR (TMA) to create custom Chip Description Files (CDF).
• Experimentally measured differential gene expression in *Schizosaccharomyces pombe* under oxidative stress.
• Employed a target-labeling protocol preserving transcript polarity and a segmentation algorithm for TMA data analysis.

Main Results:

• A high Pearson correlation coefficient (0.943) confirmed TMAs are as reliable as EMAs for quantitative expression analysis.
• Identified 510 differentially expressed transcripts (>180 nucleotides, non-overlapping ORFs) under oxidative stress using TMAs.
• Demonstrated TMAs' capability to detect strand-specific differential expression of non-annotated transcripts.

Conclusions:

• TMA hybridization data can be processed for simultaneous qualitative and quantitative analysis of both annotated and non-annotated transcripts.
• TMAs provide genome-wide coverage, adaptability to genome annotation updates, and enable strand-specific expression measurement.
• TMAs are a versatile tool for gene expression analysis across various organisms with available platforms.