The identification of novel DNA sequence motifs potentially participating in the regulation of gene transcription is a difficult task due to the small size and relative simplicity of the sequences involved. One possible way of overcoming this difficulty is to examine the promoter region of genes with similar expression profiles. Parameters of interest include similar tissue and cell-type specificity and quantitatively similar levels of mRNA in wild-type backgrounds. Tcp10b and Tctex1 are genes exhibiting these properties in that both are expressed at similar levels in pachytene spermatocytes of male mouse germ cells with little to no expression elsewhere. An analysis of the promoter region of these genes has uncovered a novel 20-nucleotide motif perfectly conserved in both. We have characterized the binding properties of this motif and show that it is specifically recognized by a 43 kD nuclear protein. The complex is highly stable and exhibits strong specificity. Furthermore, results from analyzing the sequence of several vertebrate genomes for the presence of the motif are consistent with the existence of a novel motif in the vicinity of several hundred genes.
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