Identification and functional analysis of porcine basic helix-loop-helix transcriptional factor 3 (TCF3) and its alternative splicing isoforms

•TCF3 splicing isoforms were predicted by “Tophat” analysis based on porcine RNA-seq.•Two novel TCF3 splicing isoforms TCF3A and TCF3B were identified.•Swine fever virus could reduce TCF3 expression.•TCF3(E12/E47) and TCF3B were exclusively translocated into nuclei.•TCF3A was distributed in cytoplasm.

The transcription factor 3 (TCF3) is a basic helix-loop-helix transcription factor and is essential for lymphocyte development and epithelial-mesenchymal transition. The splicing isoform, genomic organization and physiological roles of TCF3 have not been elucidated well in pig. Based on RNA-seq database, four alternative splicing isoforms were identified. Splicing isoforms TCF3(E12), TCF3(E47), and TCF3A expressed globally in porcine tissues, but TCF3B mainly expressed in spleen and endoderm derived tissues, such as pancreas and lung. The functional analysis showed that TCF3(E12), TCF3(E47), and TCF3B were translocated exclusively into nuclei, yet TCF3A was distributed in cytoplasm. The investigation of clinical specimens showed that TCF3 expression was significantly reduced in spleen tissues that were infected by classical swine fever virus (CSFV). This study is for the first time to report two novel splicing isoforms TCF3A and TCF3B, which may play an important role in lymphocyte maturation and have the correlation with CSFV evasion.