ABSTRACTConsiderable evidence indicates that the 2-cell stage is a critical period of mouse embryo development when a transition from maternal to zygotic genomic control takes place. The overall changes in the structure of the mRNA population as a result of this transition were explored using a random cDNA library of 69 clones derived from late 2-cell embryos. The prevalence of the cloned sequences was analysed by dot hybridization of the cDNA clones with labelled cDNA probes synthesized to poly(A)+ RNA from different stages of development from 1-cell through blastocyst. The number of copies of individual transcripts was quantitatively estimated by comparison to standard clones of known prevalence. About one half of the transcripts that gave a measurable reaction at the 2-cell and later stages were not represented detectably in egg RNA, suggesting that a large set of zygote-specific genes not included in the maternal gene set becomes transcriptionally active in the 2-cell embryo. Six of the cDNA clones represented Bl and B2 repeat sequences. As measured by hybridization with labelled cDNA, Bl and B2 transcripts were abundantly expressed throughout cleavage, being represented by about 105 to 106 copies per embryo. However, the developmental pattern of prevalence was different for the two transcripts suggesting that their expression is regulated independently. The results of this study corroborate previous evidence derived from protein synthetic patterns and in vitro translation experiments that a major qualitative shift in the mRNA population occurs in the 2-cell embryo.