The chromatin fiber, formed by nucleosomes attached together by linker DNA, organizes into higher-order structures such as chromatin domains and chromosomes. The domains’ compaction level plays a...Show moreThe chromatin fiber, formed by nucleosomes attached together by linker DNA, organizes into higher-order structures such as chromatin domains and chromosomes. The domains’ compaction level plays a role in the regulation of transcription and depends on chromatin folding and aggregation mechanisms. However, the relation between conformational changes of the fibers and their aggregation has not been clearly resolved yet. Here, we test in vitro conditions that favor or prevent the aggregation of chromatin fibers with linker DNA lengths of 20 bp, 25 bp, 50 bp, and 55 bp and use fluorescent correlation spectroscopy to analyze the mobility of the aggregates and their constituents. Our results show that chromatin fibers with 25, 50 and 55 bp linker DNA form micron-sized aggregates in the presence of mono and divalent cation salts. The auto-correlation and cross-correlation models yielded diffusion times in the order of seconds for early-stage aggregation. The protocols and results obtained can provide a starting point for further research on the aggregation mechanism of chromatin and its impact on DNA transcription.Show less