The transcriptional activity of nucleoids changes during plastid development, presumably due to the morphological and molecular differences of the nucleoids. Pea chloroplast nucleoids have an abundant 70-kDa protein identified as sulfite reductase (SiR) that can compact DNA. Using an in vitro transcription assay, we show here that heparin increased the transcriptional activity of chloroplast nucleoids with concomitant release of SiR. Using a fluorometric method we developed for analyzing DNA compaction, we found that the fluorescence intensity of chloroplast DNA stained with 4',6-diamidino-2-phenylindole was decreased by the addition of SiR and increased by the subsequent addition of heparin. Addition of exogenous SiR increased the compaction of isolated nucleoids, and the addition of heparin relaxed it. SiR effectively repressed the in vitro transcription activity of nucleoids and counteracted the activation by heparin. These results suggest that SiR regulates the transcriptional activity of chloroplast nucleoids through changes in DNA compaction.