Transcribed human ribosomal RNA genes are attached to the nuclear matrix

Nuclear matrices were prepared from HeLa nuclei in high or low-salt buffers. After digestion with restriction enzymes, the DNA associated with the nuclear matrix was analysed for its content of ribosomal DNA sequences (rDNA). In both salt conditions, the entire rDNA repeat unit was found to be enriched in the matrix DNA. No enrichment, however, was detected in the absence of rRNA transcription either due to treatment with actinomycin D or when cells arrested in the G0 stage were used to prepare matrices. rDNA was found to be linked to chromosomal scaffolding structures when similar experiments were performed on chromosomes. Moreover, a gradient of enrichment along the rDNA repeat unit was observed, in which the promoter-containing portion was the most highly enriched. I conclude from these experiments that the tandem repeats of rDNA are not randomly associated with matrix or scaffold structure but are probably attached at transcription complexes.