Prokaryotes do not compartmentalize their genomic DNA within a membrane-enclosed nucleus, but that doesn't mean that their genomes are not organized. In fact, bacterial DNA occupies only the central part of the cell, forming the so-called nucleoid. In addition, some loci have been observed in specific positions, especially during DNA replication and segregation. However, bacterial cells are quite small, and a detailed characterization of the nucleoid architecture has been hampered by technical limitations. Now Zhuang, Xie and colleagues have used super-resolution fluorescence microscopy to study the distribution of five nucleoid-associated proteins from Escherichia coli: HU, Fis, IHF, StpA and H-NS. Each of these proteins was tagged with the monomeric photoactivatable fluorescent protein mEos2 and expressed in E. coli. The first four proteins showed a scattered distribution within the nucleoid. In contrast, H-NS was concentrated in two clusters per nucleoid, localized near the one-quarter and three-quarter positions along the long axis of the newly-divided, rod-shaped cells. H-NS has an N-terminal domain that mediates homo-oligomerization, and the authors showed by mutagenesis that this is necessary for cluster formation. H-NS is involved in transcriptional silencing. To gain insight into how cluster organization and transcriptional control by H-NS are related, the authors followed the positions of two genes regulated by H-NS by inserting tet operator sequences upstream of the genes and expressing a fluorescent protein fused to the Tet repressor. They found that these two gene loci tended to localize with the H-NS clusters, even though they were distant from each other along the chromosome, and this localization required H-NS. However, the loci were also quite mobile and did not always localize with the H-NS cluster, indicating their dynamic nature. The pairwise proximity of several H-NS–regulated genes was independently established using chromosome conformation capture (3C) assays. Exploring the organization of the bacterial genome at such a resolution is a technical feat, and this work will lead to a better understanding of genomic architecture and regulation in bacteria. (Science 333, 1445–1449, 2011)