The proximal element is capable of determining proper temporal expression of the embryonic sea urchin U2 snRNA gene. There are two gene sets for U2 snRNA in the sea urchin L. variegatus, the U2E gene, which is expressed in oogenesis and early embryogenesis and then silenced, and the U2L gene, which is expressed constitutively. There are four major promoter elements found in both U2 snRNA genes; an essential TATA box at -25 to -30, a proximal element (PSE) at -55 required for expression, an element at -100 necessary for maximal expression, and an upstream activating sequence (UAS) necessary for maximal expression. The elements of the U2E and U2L promoters were interchanged and the effect on the temporal pattern of expression determined after microinjection of the genes into sea urchin zygotes. When the U2E PSE element was introduced into the U2L gene, the temporal pattern of expression of the gene was changed to that of the U2E gene. Converting the U2L gene proximal element into the early U2 gene proximal element by altering 14 nucleotides in the promoter also changed the temporal pattern of expression of the U2L gene. Factors that interact with the U2E PSE, detected by a gel mobility shift assay and DNaseI footprinting, were present in blastula but not late gastrula embryos. In contrast, interchanging the -100 element did not greatly affect the temporal pattern of expression, and factors that interact with the U2E gene -100 box were present in both late gastrula and blastula embryos.