Identification of diverse nerve growth factor-regulated genes by serial analysis of gene expression (SAGE) profiling

Abstract

Neurotrophic factors such as nerve growth factor (NGF) promote a wide variety of responses in neurons, including differentiation, survival, plasticity, and repair. Such actions often require changes in gene expression. To identify the regulated genes and thereby to more fully understand the NGF mechanism, we carried out serial analysis of gene expression (SAGE) profiling of transcripts derived from rat PC12 cells before and after NGF-promoted neuronal differentiation. Multiple criteria supported the reliability of the profile. Approximately 157,000 SAGE tags were analyzed, representing at least 21,000 unique transcripts. Of these, nearly 800 were regulated by 6-fold or more in response to NGF. Approximately 150 of the regulated transcripts have been matched to named genes, the majority of which were not previously known to be NGF-responsive. Functional categorization of the regulated genes provides insight into the complex, integrated mechanism by which NGF promotes its multiple actions. It is anticipated that as genomic sequence information accrues the data derived here will continue to provide information about neurotrophic factor mechanisms.

Figure 1

Distribution of NGF-promoted changes in expression of transcripts in PC12 cells as revealed by SAGE. Transcripts for which two or more tags were detected are included. Up-regulated transcripts are to the left, down-regulated transcripts to the right. Tag numbers are expressed either on a linear (A) or log (B) scale.

Figure 2

Northern blot analysis of NGF-promoted gene regulation in (A) PC12 cells and (B) PC12-cell-nnr5 derived cells with (T14) and without (nnr5) Trk expression. Total cellular RNA was isolated from cells treated without (naïve) or with NGF for 7–14 days (NGF). Ten micrograms of RNA was analyzed as described in Materials and Methods with the indicated probes. Blots were stripped and reprobed with β-actin to indicate relative loading. Ratios to side of blots indicate numbers of tags in PC12 cell SAGE analysis +/− NGF.