Ribosomal DNA is an important repeated sequence that forms the nucleolus at the interphase. Its transcription into ribosomal RNA for ribosome biogenesis also represents a transitional point for several cellular processes, including cell-cycle progression, gene-silencing, and formation of the ribonucleoprotein complex. The levels of rDNA acetylation have an important role in regulating structural changes in rDNA chromatin and transcriptional activity. Using root-tip samples from Brassica campestris, we determined that some rDNA chromatin is located in the heterochromatin regions while some is de-condensed and found in euchromatin regions. Immuno-staining results showed that histone H4K5 acetylation and H4 tetra-acetylation signals are dispersed within the euchromatin. Analysis of the promoter and exon regions of rDNA via chromatin immuno-precipitation (ChIP) revealed a connection between histone acetylation and rDNA conformation.