Summary Tight control of transposon activity is essential for the integrity of the germline. Recently, a germ cell-specific organelle, nuage, was proposed to play a role in transposon repression. To test this hypothesis, we disrupted a murine homolog of a Drosophila nuage protein Maelstrom. Effects on male meiotic chromosome synapsis and derepression of transposable elements (TEs) were observed. In the adult Mael−/− testes, LINE-1 (L1) derepression occurred at the onset of meiosis. As a result, Mael−/− spermatocytes were flooded with L1 ribonucleoproteins (RNPs) that accumulated in large cytoplasmic enclaves and nuclei. Mael−/− spermatocytes with nuclear L1 RNPs exhibited massive DNA damage and severe chromosome asynapsis even in the absence of SPO11-generated meiotic double strand breaks. This study demonstrates that MAEL, a nuage component, is indispensable for the silencing of TEs and identifies the initiation of meiosis as an important step in TE control in the male germline.

Chemical footprinting methods are widely used to probe the solution structures of nucleic acids and their complexes. Among the many available modifying reagents, hydroxyl radical is exceptional in its ability to provide nucleotide-level information on the solvent accessibility of the nucleic acid backbone. Until recently, hydroxyl radical footprinting has been limited to in vitro experiments. We describe the use of synchrotron X-radiation to generate hydroxyl radicals within cells for effective footprinting of RNA-protein complexes in vivo. This technique gives results that are consistent with in vitro footprinting experiments, with differences reflecting apparent structural changes to the RNA in vivo.

The biogenesis of new ribosomal subunits is a highly regulated process essential for cell growth. During assembly of the ribosomal subunits, ribosomal proteins join the complex in a specific hierarchy as the rRNA folds. We used hydroxyl radical footprinting to visualize changes in the structure of the 16S rRNA during assembly in real time. The results show that each domain of the 30S ribosome assembles concurrently in vitro, and that many tertiary RNA interactions and RNA‐protein interactions are established within the first 100 milliseconds. A single protein can stabilize the folded structure of the entire 16S 5' domain. However, the assembly includes both native and non‐native conformations of the 16S rRNA. Protein S16 preferentially stabilizes a native‐like assembly intermediate and promotes a conformational switch at helix 3 that stabilizes the decoding center of the 30S ribosome. In vivo footprinting experiments are beginning to reveal the conformations of immature subunits that accumulate when one or more 30S assembly factors are missing.

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