ABOVE: A long noncoding RNA helps in the process of learning in a new environment. © iStock, cokada


earning spatial elements of a new environment is important for people and animals. However, how this process occurs in the brain remains poorly understood. Long noncoding RNA (lncRNA) are abundantly expressed in the brain; although they’re predominantly studied for their roles during development, increasing evidence points to their function in the adult brain. Recently, a team from the Weizmann Institute of Science showed in a paper published in Cell Reports that Silc1, a lncRNA, regulated spatial learning in an unfamiliar environment in mice.1 Unraveling the inner workings of these complex systems could help scientists understand how the loss of learned information in neurological diseases occurs.

Rotem Perry, a neurobiologist in the lab of Igor Ulitsky, an RNA biologist and paper coauthor, paired her work studying noncoding RNA in neurons with her interest in neurogenesis. “We decided that we would try to see if there are any lncRNA that are important in regeneration,” she said.

The team showed that the expression of Silc1 influenced, influenced the expression of Sox11 during neuron regeneration.2 Sox11 is a transcription factor predominantly studied during neurogenesis in embryonic development.To explore the function of this lncRNA further, the team reviewed publicly available RNA-seq data sets and saw that Silc1 and Sox11 are highly expressed in the hippocampus. “This led us to focus on studying brain functions that are related to the hippocampus,” Ulitsky said. According to Ulitsky, spatial memory formation is a key function in this region of the brain.

The team housed mice in their regular cages and placed another group of mice in a novel environment, where they used a Barnes maze consisting of a circular raised platform with holes around the perimeter with one hole connecting to an escape tunnel. They detected Silc1 and Sox11 in the hippocampi of mouse brains using an in situ hybridization method that fluorescently tagged RNA. “This way, we could really see where it’s expressed and the changes in the novel environment,” Perry said.

Compared to mice in their usual housing, animals placed in a new environment expressed more Sox11 and Silc1. The researchers then determined if Silc1 expression drove Sox11 expression by deleting Silc1. In the absence of Silc1 in adult mice, these Sox11 targets when placed in the novel environment, and this translated to reduced production of Sox11 protein. “We were really surprised to see that it acts like an immediate early gene,” Perry said.

Fluorescent image of mouse hippocampi with red, green, and blue markers.
Silc1 deficient mice (two right columns) express less Sox11 in two regions of the hippocampus (top and bottom) compared to normal mice (two left columns).
Rotem Perry

Next, the researchers investigated the role of Silc1 and Sox11 in the hippocampus. Since spatial learning and short-term memory storage occur in the hippocampus, the team studied these parameters in normal or Silc1-deficient mice with the Morris water maze and the Barnes maze. In the Morris water maze, mice swam in a container of opaque water to find a submerged platform using visual cues placed around the tank to direct themselves. Silc1-deficient mice took longer to learn where the platform and escape tunnel were in the respective mazes compared to mice with normal Silc1 expression. However, Silc1-deficient mice and normal mice performed comparably by the end of the maze probes, indicating that Silc1 deficiency does not impair long-term memory.

“It is really cool that the long noncoding is regulated by novelty—that you have a physiological stimulus that regulates so specifically this long noncoding RNA, and that you then also can discriminate between, for example, two types of memories that it affects: spatial memory, but not long term memory,” said Jeroen Pasterkamp, a translational neuroscientist at University Medical Center Utrecht who was not involved in the study.

To identify how Silc1 and Sox11 expressions influence spatial learning, the group overexpressed Sox11 in mice, performed RNA sequencing, and identified a subset of genes activated by Sox11. Many of these were also upregulated during embryonic development. In the absence of Silc1, these Sox11 targets are not expressed when the animals are introduced to a new environment.

In a follow up analysis, the team performed single-nucleus RNA sequencing followed by gene ontology analysis on hippocampus tissues from normal and Silc1-deficient mice to explore the functions of Sox11-regulated genes. They showed that many of these genes corresponded to activities such as synaptic transmission, axon guidance, and dendritic localization. They concluded that many of the pathways that Sox11 uses for neurogenesis during development also are used for learning in the adult brain, at which time their activity through Sox11 depends on Silc1.

“We see that a program that is typically thought to be happening only as the brain is growing and as it is forming is reactivated during memory formation,” said Ulitsky. “But on the other hand, we see that this long noncoding RNA, which is activating this program, is actually not found in the embryo at all.”


  1. Perry RB-T, et al. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation. Cell Rep. 2023;42(10):113168
  2. Perry RB-T, et al. Regulation of neuroregeneration by long noncoding RNA. Molec Cell. 2018;72:553-567
  3. Tsang SM, et al. Regulatory roles for SOX11 in development, stem cells, and cancer. Semin Cancer Biol. 2020;67(1):3-11