Abstract

Neuronal activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. A large number of genes regulated by different neuronal plasticity inducing pathways have been identified, but altered gene expression levels represent only part of the complexity of the activity-regulated transcriptional program. Alternative splicing, the differential inclusion and exclusion of exonic sequence in mRNA, is an additional mechanism that is thought to define the activity-dependent transcriptome. Here, we present a genome wide microarray-based survey to identify exons with increased expression levels at 1, 4 or 8 h following neuronal activity in the murine hippocampus provoked by generalized seizures. We used two different bioinformatics approaches to identify alternative activity-induced exon usage and to predict alternative splicing, ANOSVA (ANalysis Of Splicing VAriation) which we here adjusted to accommodate data from different time points and FIRMA (Finding Isoforms using Robust Multichip Analysis). RNA sequencing, in situ hybridization and reverse transcription PCR validate selected activity-dependent splicing events of previously described and so far undescribed activity-regulated transcripts, including Homer1a, Homer1d, Ania3, Errfi1, Inhba, Dclk1, Rcan1, Cda, Tpm1 and Krt75. Taken together, our survey significantly adds to the comprehensive understanding of the complex activity-dependent neuronal transcriptomic signature. In addition, we provide data sets that will serve as rich resources for future comparative expression analyses.

Highlights

  • Neurons go through activity-dependent alterations in their molecular composition and structure in order to fine-tune their synaptic strength

  • Analysis of neuronal activity‐regulated genes We triggered seizures in mice to induce strong synchronous neuronal activity in the hippocampus for a comprehensive analysis of alternatively spliced gene transcripts induced by neuronal activity

  • RNA extracted from one hippocampus was hybridized to one microarray

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Summary

Introduction

Neurons go through activity-dependent alterations in their molecular composition and structure in order to fine-tune their synaptic strength. Such neuronal plasticity plays a vital role during a critical period in the development of the nervous system [1]. Changes in gene expression levels represent only one aspect of the complexity of the transcriptional signature of neurons. Neuronal activity is thought to regulate splicing of a number of induced transcripts [10, 11]. Most surveys focused only on gene expression levels and the description of neuronal activity-regulated splicing events is incomplete

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