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• 1. [Article] Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times

  Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of ...

  Citation × Citation Citation Abstract Copy Title: Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times Author: Bernier, Jeremiah C. Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of Chinook into two broad types or runs, fall and spring, named for the time of year in which they migrate to freshwater. Migration time in Chinook has a strong genetic component, and historically, fall and spring runs were spatially and temporally isolated in watersheds. Using a population of Chinook from California’s Central Valley, I sought to examine gene regulation that results in differential run-timing. Functional genomics has proven to be powerful in distinguishing genes differentially expressed between alternate behaviors in other systems and I used the technique LongSAGE to examine genes differentially regulated between fall and spring run Chinook during freshwater migration. I constructed three LongSAGE libraries from the brains of a spring, fall and ocean sample and observed 221 differentially expressed tags. Using expressed sequence tag (EST) libraries from Atlantic salmon (Salmo salar) and rainbow trout (O. mykiss), I was able to assign putative functions to 59% of differentially expressed tags. Additionally, I tested the expression levels of seven genes in the brains of 8 additional individuals from both runs and found none significantly differentially expressed between fall and spring runs. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future gene expression research into reproduction and migration times, as well as physiology of migrating salmon. Title: Neural gene expression profiling in chinook salmon (Oncorhynchus tshawytscha) of alternate run times Author: Bernier, Jeremiah C. Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Differential return times to freshwater have segregated populations of Chinook into two broad types or runs, fall and spring, named for the time of year in which they migrate to freshwater. Migration time in Chinook has a strong genetic component, and historically, fall and spring runs were spatially and temporally isolated in watersheds. Using a population of Chinook from California’s Central Valley, I sought to examine gene regulation that results in differential run-timing. Functional genomics has proven to be powerful in distinguishing genes differentially expressed between alternate behaviors in other systems and I used the technique LongSAGE to examine genes differentially regulated between fall and spring run Chinook during freshwater migration. I constructed three LongSAGE libraries from the brains of a spring, fall and ocean sample and observed 221 differentially expressed tags. Using expressed sequence tag (EST) libraries from Atlantic salmon (Salmo salar) and rainbow trout (O. mykiss), I was able to assign putative functions to 59% of differentially expressed tags. Additionally, I tested the expression levels of seven genes in the brains of 8 additional individuals from both runs and found none significantly differentially expressed between fall and spring runs. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future gene expression research into reproduction and migration times, as well as physiology of migrating salmon. Close

• 2. [Article] Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression

  Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been ...

  Citation × Citation Citation Abstract Copy Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Title: Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression Author: Banks, Michael A., McArthur, Andrew G., Birkeland, Shanda R., Bernier, Jeremiah C., Cipriano, Michael J. Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data. Close