We have examined DNase I sensitivity of .betha.-tubulin and flagellar calmodulin genes which are transiently and coordinately activated differentiation of Naegleria gruberi amebae into flagellates. The DNase I sensitivity of .betha.-tubulin and flagellar calmodulin genes changed in parallel with the changes in transcriptional activity of the respective genes during differentiation. The two genes were resistant to DNase I inamebae stage when transcription of the two genes was inactive. Forthy minutes after initiation of differentiation, when the two genes were most actively being transcribed, the two genes showed the highest sensitsivity to DNase I. One hundred and twenty minutes after initiation, the differentiation was completed and transcriptional activity of the two genes decreased to a low level. At this stage, the two genes were resistant to DNase I treatment like the ones at the amebae stage. This change in the DNase I sensitivity of the two genes was not observed when transcription of the two genes was blocked by adding cycloheximide at the beginning of differentiation.