Open Access Research article

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia

Dieter Newrzella1, Payam S Pahlavan2, Carola Krüger1, Christine Boehm1, Oliver Sorgenfrei1, Helmut Schröck2, Gisela Eisenhardt1, Nadine Bischoff1, Gerhard Vogt1, Oliver Wafzig1, Moritz Rossner3, Martin H Maurer2, Holger Hiemisch1, Alfred Bach1, Wolfgang Kuschinsky2 and Armin Schneider1*

Author Affiliations

1 Sygnis Bioscience, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany

2 Department of Physiology, University of Heidelberg, Im Neuenheimer Feld 326, Heidelberg, Germany

3 MPI for Experimental Medicine, Hermann-Rein-Str. 3, Göttingen, 69120, Germany

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BMC Genomics 2007, 8:370  doi:10.1186/1471-2164-8-370

Published: 15 October 2007



The different physiological repertoire of CA3 and CA1 neurons in the hippocampus, as well as their differing behaviour after noxious stimuli are ultimately based upon differences in the expressed genome. We have compared CA3 and CA1 gene expression in the uninjured brain, and after cerebral ischemia using laser microdissection (LMD), RNA amplification, and array hybridization.


Profiling in CA1 vs. CA3 under normoxic conditions detected more than 1000 differentially expressed genes that belong to different, physiologically relevant gene ontology groups in both cell types. The comparison of each region under normoxic and ischemic conditions revealed more than 5000 ischemia-regulated genes for each individual cell type. Surprisingly, there was a high co-regulation in both regions. In the ischemic state, only about 100 genes were found to be differentially expressed in CA3 and CA1. The majority of these genes were also different in the native state. A minority of interesting genes (e.g. inhibinbetaA) displayed divergent expression preference under native and ischemic conditions with partially opposing directions of regulation in both cell types.


The differences found in two morphologically very similar cell types situated next to each other in the CNS are large providing a rational basis for physiological differences. Unexpectedly, the genomic response to ischemia is highly similar in these two neuron types, leading to a substantial attenuation of functional genomic differences in these two cell types. Also, the majority of changes that exist in the ischemic state are not generated de novo by the ischemic stimulus, but are preexistant from the genomic repertoire in the native situation. This unexpected influence of a strong noxious stimulus on cell-specific gene expression differences can be explained by the activation of a cell-type independent conserved gene-expression program. Our data generate both novel insights into the relation of the quiescent and stimulus-induced transcriptome in different cells, and provide a large dataset to the research community, both for mapping purposes, as well as for physiological and pathophysiological research.