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Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex.

Stansberg C, Ersland KM, van der Valk P, Steen VM - BMC Neurosci (2011)

Bottom Line: A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb.We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr E. Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Norway. Christine.Stansberg@uib.no

ABSTRACT

Background: The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.

Results: In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.

Conclusions: Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

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Validation of regional enrichment by QPCR. Relative gene expression as demonstrated by TaqMan QPCR for 20 selected genes enriched in rat A) FMCx, B) TCx and C) OCx. The diagrams display mean values for up to twelve replicates from each region, including left and right hemispheres from the three rats included in the microarray study as well as three additional rats included for validation purposes. Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. ANOVA (p < 0.05) confirmed significant regional enrichment across cortical regions for all genes, with p-values ranging from 10-5 - 10-11 for the FMCx genes, 10-3 - 10-12 for the TCx genes and 10-2 - 10-6 for the OCx genes. Expression of Crim1 and Atoh7 could not be detected by their respective TaqMan assays. Details on TaqMan assays and statistical results are included in Additional file 4. FMCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex.
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Figure 5: Validation of regional enrichment by QPCR. Relative gene expression as demonstrated by TaqMan QPCR for 20 selected genes enriched in rat A) FMCx, B) TCx and C) OCx. The diagrams display mean values for up to twelve replicates from each region, including left and right hemispheres from the three rats included in the microarray study as well as three additional rats included for validation purposes. Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. ANOVA (p < 0.05) confirmed significant regional enrichment across cortical regions for all genes, with p-values ranging from 10-5 - 10-11 for the FMCx genes, 10-3 - 10-12 for the TCx genes and 10-2 - 10-6 for the OCx genes. Expression of Crim1 and Atoh7 could not be detected by their respective TaqMan assays. Details on TaqMan assays and statistical results are included in Additional file 4. FMCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex.

Mentions: Among the 65 regionally enriched genes, we selected a subset of 22 genes for more detailed analysis (indicated by bold letters in Figure 1), including an independent validation by quantitative real-time PCR. Since most of our 65 regionally enriched genes were validated by independent analysis on a second microarray platform, we considered it unnecessary to validate all genes by QPCR. We used all cortical samples from the three original rats included in the microarray experiment, together with corresponding samples from three additional rats. As mentioned above for the microarray analyses, corresponding left and right samples from the same cortical region were treated as individual replicates. The QPCR analyses confirmed the regional enrichment of all but two of these 22 genes (Atoh7 and Crim1), whose transcripts could not be amplified in any of the cortical samples (Figure 5). Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. Details on TaqMan assays and statistical results are included in Additional file 4.


Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex.

Stansberg C, Ersland KM, van der Valk P, Steen VM - BMC Neurosci (2011)

Validation of regional enrichment by QPCR. Relative gene expression as demonstrated by TaqMan QPCR for 20 selected genes enriched in rat A) FMCx, B) TCx and C) OCx. The diagrams display mean values for up to twelve replicates from each region, including left and right hemispheres from the three rats included in the microarray study as well as three additional rats included for validation purposes. Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. ANOVA (p < 0.05) confirmed significant regional enrichment across cortical regions for all genes, with p-values ranging from 10-5 - 10-11 for the FMCx genes, 10-3 - 10-12 for the TCx genes and 10-2 - 10-6 for the OCx genes. Expression of Crim1 and Atoh7 could not be detected by their respective TaqMan assays. Details on TaqMan assays and statistical results are included in Additional file 4. FMCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040714&req=5

Figure 5: Validation of regional enrichment by QPCR. Relative gene expression as demonstrated by TaqMan QPCR for 20 selected genes enriched in rat A) FMCx, B) TCx and C) OCx. The diagrams display mean values for up to twelve replicates from each region, including left and right hemispheres from the three rats included in the microarray study as well as three additional rats included for validation purposes. Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. ANOVA (p < 0.05) confirmed significant regional enrichment across cortical regions for all genes, with p-values ranging from 10-5 - 10-11 for the FMCx genes, 10-3 - 10-12 for the TCx genes and 10-2 - 10-6 for the OCx genes. Expression of Crim1 and Atoh7 could not be detected by their respective TaqMan assays. Details on TaqMan assays and statistical results are included in Additional file 4. FMCx, fronto-medial cortex; TCx, temporal cortex; OCx, occipital cortex.
Mentions: Among the 65 regionally enriched genes, we selected a subset of 22 genes for more detailed analysis (indicated by bold letters in Figure 1), including an independent validation by quantitative real-time PCR. Since most of our 65 regionally enriched genes were validated by independent analysis on a second microarray platform, we considered it unnecessary to validate all genes by QPCR. We used all cortical samples from the three original rats included in the microarray experiment, together with corresponding samples from three additional rats. As mentioned above for the microarray analyses, corresponding left and right samples from the same cortical region were treated as individual replicates. The QPCR analyses confirmed the regional enrichment of all but two of these 22 genes (Atoh7 and Crim1), whose transcripts could not be amplified in any of the cortical samples (Figure 5). Gene expression levels in the samples from the three additional rats completely correlated with data from the original rats. Details on TaqMan assays and statistical results are included in Additional file 4.

Bottom Line: A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb.We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr E. Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Norway. Christine.Stansberg@uib.no

ABSTRACT

Background: The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.

Results: In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.

Conclusions: Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

Show MeSH