Transcriptome networks in the mouse retina: An exon level BXD RI database

Area of Science:

• Genomics
• Ophthalmology
• Molecular Biology

Background:

• Gene expression differences create diverse retina phenotypes.
• These differences may influence susceptibility to retinal injury and disease.

Purpose of the Study:

• To define the retina transcriptome in the BXD RI strain set.
• To investigate protein-coding genes, non-coding RNAs, and microRNAs using the Affymetrix Mouse Gene 2.0 ST array.
• To present these data in an interactive database on the GeneNetwork website.

Main Methods:

• Quantified mRNA levels of the transcriptome from retinas using the Affymetrix Mouse Gene 2.0 ST array.
• Utilized data from male and female mice across 52 BXD RI strains, parental strains, and a reciprocal cross.
• Integrated data with the GeneNetwork platform and the CDMRP Normal Retina Database.

Main Results:

• Developed a comprehensive resource for mapping, graphing, analyzing, and testing complex genetic networks in the retina.
• Identified quantitative trait loci (QTLs) contributing to expression differences and linked them to ocular phenotypes.
• Extracted transcriptome signatures for retinal cells and defined genetic networks crucial for normal retina maintenance.
• Examined differentially expressed exons within individual genes.

Conclusions:

• High variability in mRNA levels among BXD RI strains enables identification of expression networks underlying retina structure and function differences.
• This database will be instrumental in defining molecular changes following retinal blast injury.