Large-scale chromatin structure is the higher-order folding of chromatin on the scale of several hundred kilobases. Little is known about this folding, but the structures must influence transcription, replication and repair of DNA. To learn more about these structures, we previously examined transcriptionally active domains of 400 2000 kb by light microscopy. We found that several different domains exhibit similar structures in light microscope images, namely a series of adjacent puncta or "beads" approximately 0.5 microns in diameter. When these same domains are transcriptionally inactive, only one punctum or "bead" is detected. Thus transcription induces a decondensation from single beaded to multi-beaded structures. We have now examined the association of polyermase II with these beaded structures using the tandem array system described in the transcription factor mobility project. We find that the polymerase also forms "beads" that associate with, but do not directly overlay the chromatin beads described above. Although a direct comparison of polymerase with chromatin structure has not been reported before, the tendency of polymerase to cluster has been widely reported, and has led to the model that transcription occurs in these clusters or "factories" by movement of the DNA through the factory, rather than movement along the DNA of the polymerase. This model predicts polymerase factories should be surrounded by recently transcribed DNA. We have tested this by developing a new method for preserving fragile DNA structures in cells and found that the polymerase factories associated with the tandem array are in fact surrounded by DNA from the tandem array. This DNA surrounding the factory seems to have been recently transcribed, since it is marked by a certain histone modification associated with recently transcribed DNA. These observations provide new support to the hypothesis that transcription occurs by movement of DNA through a stationary polymerase.