DNA topoisomerase TOP1a plays a specific role in Arabidopsis plants development and is required for stem cell regulation in the shoot and floral meristems. Recently, morphological features independent of meristem functioning have been described for fas5, a new mutation which leads to a premature termination of transcription and loss of a functionally significant C-terminal domain of topoisomerase I. We performed RNA sequencing to identify differentially expressed genes in the apices of young inflorescences of fas5 and Dijon-M plants to clarify the effects of fas5 on bolting initiation and flower development. This analysis showed that mutation caused changes in the expression level of 3901 genes. RNA sequencing revealed the activation of the shade avoidance response pathways in fas5 and the repression of genes controlling floral meristem identity and organ morphogenesis, thus indicating a wider TOP1a role in plant development.