Natural variation and genetic covariance in adult hippocampal neurogenesis

Abstract

Adult hippocampal neurogenesis is highly variable and heritable among laboratory strains of mice. Adult neurogenesis is also remarkably plastic and can be modulated by environment and activity. Here, we provide a systematic quantitative analysis of adult hippocampal neurogenesis in two large genetic reference panels of recombinant inbred strains (BXD and AXB/BXA, n = 52 strains). We combined data on variation in neurogenesis with a new transcriptome database to extract a set of 190 genes with expression patterns that are also highly variable and that covary with rates of (i) cell proliferation, (ii) cell survival, or the numbers of surviving (iii) new neurons, and (iv) astrocytes. Expression of a subset of these neurogenesis-associated transcripts was controlled in cis across the BXD set. These self-modulating genes are particularly interesting candidates to control neurogenesis. Among these were musashi (Msi1h) and prominin1/CD133 (Prom1), both of which are linked to stem-cell maintenance and division. Twelve neurogenesis-associated transcripts had significant cis-acting quantitative trait loci, and, of these, six had plausible biological association with adult neurogenesis (Prom1, Ssbp2, Kcnq2, Ndufs2, Camk4, and Kcnj9). Only one cis-acting candidate was linked to both neurogenesis and gliogenesis, Rapgef6, a downstream target of ras signaling. The use of genetic reference panels coupled with phenotyping and global transcriptome profiling thus allowed insight into the complexity of the genetic control of adult neurogenesis.

Fig. 1.

Flow-chart diagram of the experimental design and the underlying rationale. The study combines a classical linkage study with expression genetics, that is, the genetics of how genes control genes. At the end of the present experiment stands a number of genes whose variation in expression across the BXD breeding panel is correlated with adult hippocampal neurogenesis.

Fig. 2.

PROL and number of new NEUR in BXD and AXB/BXA strains of mice. (A) The raw data as assessed by Ki67 immunohistochemistry in the subgranular zone of the dentate gyrus. (B) The residuals after correction for age effects (square transformation). (C) The raw data as assessed by BrdUrd and NeuN immunohistochemistry in the subgranular zone of the dentate gyrus, 4 weeks after the BrdUrd injections. (D) The residuals after correction for age effects (log transformation). The analogous information for SURV and ASTR is found in Fig. 5. (E–G), Predictive power of PROL and SURV for NEUR and ASTR. Regression analysis of the residuals was performed. (E) Cell proliferation was significantly correlated with the number of new NEUR (P = 0.0006), but r2 = 0.193. (F) SURV, as assessed by the total number of BrdUrd-labeled cells, irrespective of their phenotype, was also significantly correlated with the number of new NEUR(P <0.001), but, here, r2 = 0.847, indicating a high predictive power of SURV for NEUR. (G) This link was not apparent for ASTR, where SURV was not correlated with NEUR (P = 0.5628; r2 = 0.005).

Fig. 3.

Interval mapping for PROL, SURV, NEUR, and ASTR. Age-corrected residuals for the three phenotypes were analyzed in WebQTL. The entire genome is depicted from the first base of chromosome 1 on the left to the last base on chromosome X on the right. The colored lines indicate the LRS score at each genome segment. Below are interval mappings for five of the cis-acting candidates with significant QTL colocalizing with peaks in the linkage curves for the neurogenesis phenotypes. The yellow bars are results of a bootstrap analysis; higher bars indicate higher stability of the LRS score against random permutations of the data. LRS levels of significance (P < 0.05) were determined for the individual data sets and marked by the dashed lines. The thin red line shows additive effects: Negative values indicate an influence of the C57 allele, positive values of DBA.

Fig. 4.

Conceptual scheme highlighting the relationship between genomic factors, gene expression, and measured phenotypes of adult neurogenesis.