Messenger RNA differntial display strategies in birds and amphibians

Abstract

As an inroad to the discovery of genes involved in important biological activities, various techniques have been developed for detecting genes based on their expression levels. Arbitrary amplification of different messenger RNA (mRNA) populations and their comparison on display autoradiograms made mRNA differential display one of the most straightforward approaches to identification of differentially regulated mRNAs. Over the past decade this strategy has been employed in many in vitro and in vivo systems. The use of the method in bird and amphibian model systems is reviewed here, emphasizing several unique combinations of model system and design of differential display screen.

Multi-Tissue Microarray Analysis Identifies a Molecular Signature of Regeneration

“…The microarrays probed 1876 genes, with over 90% of these sequences derived from mRNA differential display screens of regenerating newt limbs, tails and brain tissue collected during spinal cord regeneration [25]–[27], while the remaining probes represented all other newt sequences available from GenBank at the time of array design. Unlike other approaches, this array customization allowed for a significant enrichment of regeneration-specific gene activities.…”

“…This microarray contained all probes present on Microarray A, with additional, newly acquired sequences. Over 90% of N. viridescens genes in both arrays were cloned from mRNA isolated from regenerating tissues during differential display analysis [25]–[27]. In some cases, it was unknown which strand was the coding strand; therefore, a set of probes was generated that could hybridize to both strands.…”

“…Additionally, these investigations typically considered a large initial gene set, with subsequent analytical effort primarily devoted to the discovery of those genes showing high levels of differential expression. In contrast to these earlier approaches, we developed Agilent microarrays containing oligonucleotides largely derived from the sequences of genes identified in previous mRNA differential display screens of regenerating newt limbs, tails and brain tissue collected during spinal cord regeneration performed by the Simon and Odelberg laboratories (described in [25]–[27]). The pre-selection for cDNAs enriched in regenerative programs and the high number of replicates placed on our custom arrays allowed for substantial qualitative and accurate quantitative analyses that have not been achieved previously.…”

Evidence for Proximal to Distal Appendage Amputation Site Effects from Global Gene Expression Correlations Found in Newt Microarrays

“…Among those, the North American Eastern newt (N. viridescens) represents an important model system for studying the complex biological process of tissue and limb regeneration following limb loss [2][3][4].…”

“…Nearly 70% of the cDNAs on the Agilent chip were from unknown and uncharacterized sequences that were not represented in the public databases. The sequences had been compiled by the Odelberg (University of Utah) and Simon (Northwestern University) laboratories using mRNA differential display-based selection [2][3][4] and Genbank searches.…”