Brn-3a long and short isoforms are known to be encoded by two distinct mRNA transcripts derived from a single gene. Here we report that transcription of the two isoforms is differentially regulated. The short isoform has its own promoter, though many elements in the 5' regulatory region are shared. The protein product of the EWS gene, translocations of which are associated with the Ewing's sarcoma family of tumours, is known to interact with Brn-3a via a direct protein-protein interaction. Here we show that EWS also regulates Brn-3a expression in an isoform-specific manner. The implications of these results are discussed in terms of the functional role of EWS and the distinct functional activities of the two isoforms of Brn-3a. (C) 2004 Elsevier Inc. All rights reserved.