Functional tests, performed by microinjection into Xenopus laevis oocytes, show that a DNA fragment containing the modulator of the early histone H2A gene of Paracentrotus lividus enhances transcription of a reporter gene when located, in the physiological orientation, upstream of the tk basal promoter. Gel retardation and DNase I footprinting assays further reveal that the H2A modulator contains at least two binding sites [upstream sequence elements 1 and 2 (USE 1 and USE 2)] for nuclear factors extracted from sea urchin embryos, which actively transcribe the early histone gene set. Interestingly, USE 1 is highly homologous to a cis-acting element previously identified in the H2A modulator of Psammechinus milians [Grosschedl, R., Machler, M., Rohrer, U. & Birnstiel, M. L. (1983) Nucleic Acids Res. 11, 8123-8136]. Finally, a cloned oligonucleotide containing the USE 1 sequence competes efficiently in Xenopus oocytes with the H2A modulator to prevent enhancement of transcription of the reporter gene. From these results, we conclude that USE 1 and perhaps USE 2 in the H2A modulator are upstream transcriptional elements that are recognized by trans-acting factors common to Xenopus and sea urchin.The sea urchin genome contains several histone gene families that encode the protein subtypes of sperm (S-type) and of cleavage, early, and late stage embryo (1). The synthesis of specific histone protein variants during development is the result of regulatory mechanisms that operate at both the transcriptional and posttranscriptional level (2). The early histone genes in all sea urchin species are tandemly repeated 300-600 times and are organized in quintets (3,4). Transcription of this gene set occurs upon meiotic maturation and soon after fertilization (5-7). Newly synthesized early histone mRNAs accumulate at the 32-to 128-cell stage. Their transcription is shut off in mesenchyme blastula embryos (8-10). The transition from a transcriptionally active to an inactive state of the early histone genes is accompanied by structural alterations of their chromatin arrangement (11-13).Molecular genetic analysis of many polymerase II promoters has revealed that optimal and accurate initiation of transcription requires a cooperative interaction of transacting factors with multiple cis-acting transcriptional elements (14)(15)(16)(17).Recent studies on the factors involved in the transcriptional control of the sea urchin histone H1 and H2B genes have identified basal and ontogenic transcriptional elements involved in the transition from early to late gene expression during development (18,19). Furthermore, they have shown that an embryo-specific repressor element, the CCAAT displacement factor, prevents the interaction of a positive trans-acting factor with the CCAAT box ofthe sperm-specific H2B-1 gene (20) and in so doing may block transcription in the embryo.We have focused our attention on the early H2A gene ofthe sea urchin Paracentrotus lividus for several reasons. The 5' flanking region of this gene contains, upstream...