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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

Expression and sequences of genes encoding glutamate receptors and transporters in primate retina determined using 3'-end amplification polymerase chain reaction.

PURPOSE: Our long-term goal is to compare how expression of glutamate receptor and non-vesicular transporter subunits differs between single neurons in the primate retina. Here we set out to ascertain general expression in the retina of Macaca fascicularis using a robust technique suitable for both levels of analysis. We constructed full-complement cDNAs from whole retina RNA using a protocol optimized for detection of even low-abundance transcripts and for transcripts of various lengths. We probed these libraries for expression of genes encoding the AMPA- (GluR1-4) and kainate-sensitive (GluR5-7, KA1-2) ionotropic glutamate receptors, the metabotropic glutamate receptors (mGluR1-8), and five non-vesicular glutamate transporters (EAAT1-5) in the macaque retina and brain and determined large portions of coding sequences for each. We also asked whether each gene can be detected in cDNA generated from a limited amount of RNA extracted from an aldehyde-fixed retinal slice, a technique useful for probing gene expression in tissue used for histological studies. METHODS: We constructed full-length cDNA from RNA harvested from the macaque retina using a modified version of the 3'-end amplification (TPEA) technique of Dixon et al. With this technique, the 3' region is amplified arbitrarily using multiple primers to produce amplified cDNA containing as diverse and complete sample of genes as possible. We probed the cDNA for expression of glutamate receptors and non-vesicular transporters using gene-specific RT-PCR and assembled sequences from the reaction products using a series of overlapping primer pairs. We also used TPEA to compare expression in a small amount of RNA extracted from a fixed retinal slice. RESULTS: Macaque retinal cDNA created using TPEA contains a high abundance of transcripts of various lengths. Gene-specific PCR using primers designed against human sequences indicates expression for all GluR, mGluR, and non-vesicular transporter subunits for which we probed. Expression patterns were similar between two different macaque retinas, but different in brain. Several differences also exist between macaque and human brain. For some subunits, this is the first demonstration of expression in the macaque retina. The expression pattern obtained probing cDNA libraries generated from fixed tissue RNA with a different primer set was similar to that for fresh tissue. We sequenced between 1865 (mGluR8a) and 3697 (mGluR1) total nucleotides for each macaque gene and obtained complete coding sequences for GluR1-7, mGluR3 and mGluR4. A comparison with the corresponding human sequences reveal that the coding region of macaque GluR6 demonstrates the highest homology with only 26 nucleotide substitutions (99% homology), while mGluR4 demonstrates the lowest with 68 substitutions (97.5%). CONCLUSIONS: Neural tissue cDNA created using TPEA contains diverse transcripts of varying size, abundance, and homology. We established using TPEA the expression of all nine AMPA- and kainate-sensitive GluRs, all eight mGluRs and all five non-vesicular glutamate transporters and found that expression differs between macaque retina, macaque brain and human brain. The nucleotide sequences for the coding regions differed moderately between the human and macaque genes. We also found a similar expression pattern in a smaller amount of RNA extracted from a fixed retinal slice. Thus, this technique could be useful for comparing gene expression in cells extracted from fixed tissue pre-labeled using specific markers.[1]


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