Expression profiling and analysis of transcription factors for neuronal differentiation from stem cells

Dong Mi Shin1, Joon Ik Ahn2, Ki Hwan Lee, Young Seek Lee, Yong Sung Lee, Hanyang University;, Hanyang University

To identify transcription factors that may play an important role in the differentiation of embryonic stem (ES) cells to neurons, high throughput gene expression experiment and computational analysis were performed. Using five-stage lineage selection method, we induced neuronal differentiation from mouse embryonic stem cells and compared the gene expression profiles between different differentiation stages. Out of 10,368 genes, 1,633 (16%) genes were differentially expressed at least one or more stages. A set of genes whose frequency of occurrence of its consensus bining sequence in the promotor regions of the above 1,633 significantly changed genes was higher than the promotor regions of a rondom pool of genes was selected. All genes in the Genbank Refseq section having more than 5000 bp continuous regions upstream of the first exon start site were used to construct the promoter refernece database. The promoter region sequences of the selected genes were checked for transcription factor binding sites by running Match against TRANSFAC MATRIX libraries. Our result suggest large numbers of transcription factors which include some novel transcription factors as well as those previously known to be involved in differentiation signaling.