To get a handle on which genes play a key role in this process, Ramamoorthi and Lin trained mice in a contextual fear-conditioning paradigm, which is thought to be dependent on new gene transcription in the dorsal hippocampus (which corresponds to the posterior hippocampus in primates).
In this test, mice freeze in anticipation of a mild-foot shock received during the training period.

The researchers looked at the expression of genes in the dorsal hippocampus of the mice just after they had completed the training.

“We saw that Npas4 is induced specifically with learning. That was very encouraging,” said Lin. Neuronal PAS domain protein 4 (Npas4) is an activity-dependent transcription factor and a known immediate early gene.
The researchers were surprised to find that Npas4 expression only rose in cells in the CA3 region of the hippocampus. “Contextual conditioning requires the CA3 region, so that told us this gene was special,” said Lin. Other immediate early genes such as c-Fos and Arc, which have been implicated in long-term memory, are not CA3 specific, according to Lin. “The specificity of Npas4 induction means that it could be an important marker for cells undergoing information processing,” said Ramamoorthi.
In fact, mice genetically engineered to lack Npas4 in the CA3 region froze less than wild-type animals in the fear-conditioning test.

If and how Npas4 influences memory is unclear, but it reached its peak expression in the CA3 region in mice 30 minutes after completing contextual fear conditioning, one hour before c-Fos is turned on.
“That is another indication that Npas4 is a critical factor for initiating memory programs” said Ramamoorthi.
Having a marker for cells undergoing memory processing will allow researchers to study what other genes are turned on or off in those cells.
“We want to identify the hierarchical cascade of genes regulated downstream of Npas4,” said Lin. “We want to get a better understanding of this genetic cascade after learning takes place.”